Proteins Associated with cell growth, differentiation, and death

ABSTRACT

The invention provides human proteins associated with cell growth, differentiation, and death (CGDD) and polynucleotides which identify and encode CGDD. The invention also provides expression vectors, host cells, antibodies, agonists, and antagonists. The invention also provides methods for diagnosing, treating, or preventing disorders associated with aberrant expression of CGDD.

TECHNICAL FIELD

[0001] This invention relates to nucleic acid and amino acid sequences of proteins associated with cell growth, differentiation, and death and to the use of these sequences in the diagnosis, treatment, and prevention of cell proliferative disorders including cancer, developmental disorders, neurological disorders, autoimmune/inflammatory disorders, reproductive disorders, and disorders of the placenta, and in the assessment of the effects of exogenous compounds on the expression of nucleic acid and amino acid sequences of proteins associated with cell growth, differentiation, and death.

BACKGROUND OF THE INVENTION

[0002] Human growth and development requires the spatial and temporal regulation of cell differentiation, cell proliferation, and apoptosis. These processes coordinately control reproduction, aging, embryogenesis, morphogenesis, organogenesis, and tissue repair and maintenance. At the cellular level, growth and development is governed by the cell's decision to enter into or exit from the cell division cycle and by the cell's commitment to a terminally differentiated state. These decisions are made by the cell in response to extracellular signals and other environmental cues it receives. The following discussion focuses on the molecular mechanisms of cell division, embryogenesis, cell differentiation and proliferation, and apoptosis, as well as disease states such as cancer which can result from disruption of these mechanisms.

[0003] Cell Cycle

[0004] Cell division is the fundamental process by which all living things grow and reproduce. In unicellular organisms such as yeast and bacteria, each cell division doubles the number of organisms. In multicellular species many rounds of cell division are required to replace cells lost by wear or by programmed cell death, and for cell differentiation to produce a new tissue or organ. Progression through the cell cycle is governed by the intricate interactions of protein complexes. This regulation depends upon the appropriate expression of proteins which control cell cycle progression in response to extracellular signals, such as growth factors and other mitogens, and intracellular cues, such as DNA damage or nutrient starvation. Molecules which directly or indirectly modulate cell cycle progression fall into several categories, including cyclins, cyclin-dependent protein kinases, growth factors and their receptors, second messenger and signal transduction proteins, oncogene products, and tumor-suppressor proteins.

[0005] Progression through the cell cycle is governed by the intricate interactions of protein complexes. This regulation depends upon the appropriate expression of proteins which control cell cycle progression in response to extracellular signals, such as growth factors and other mitogens, and intracellular cues, such as DNA damage or nutrient starvation. Molecules which directly or indirectly modulate cell cycle progression fall into several categories, including cyclins, cyclin-dependent protein kinases, growth factors and their receptors, second messenger and signal transduction proteins, oncogene products, and tumor-suppressor proteins.

[0006] The entry and exit of a cell from mitosis is regulated by the synthesis and destruction of a family of activating proteins called cyclins. Cyclins act by binding to and activating a group of cyclin-dependent protein kinases (Cdks) which then phosphorylate and activate selected proteins involved in the mitotic process. Cyclins are characterized by a large region of shared homology that is approximately 180 amino acids in length and referred to as the “cyclin box” (Chapman, D. L. and Wolgemuth, D. J. (1993) Development 118:229-40). In addition, cyclins contain a conserved 9 amino acid sequence in the N-terminal region of the molecule called the “destruction box”. This sequence is believed to be a recognition code that triggers ubiquitin-mediated degradation of cyclin B (Hunt, T. (1991) Nature 349:100-101). Several types of cyclins exist (Ciechanover, A. (1994) Cell 79:13-21). Progression through G1 and S phase is driven by the G1 cyclins and their catalytic subunits, including Cdk2-cyclin A, Cdk2-cyclin E, Cdk4-cyclin D and Cdk6-cyclin D. Progression through the G2-M transition is driven by the activation of mitotic CDK-cyclin complexes such as Cdc2-cyclin A, Cdc2-cyclin B1 and Cdc2-cyclin B2 complexes (reviewed in Yang, J. and Kornbluth, S. (1999) Trends in Cell Biology 9:207-210).

[0007] Cyclins are degraded through the ubiquitin conjugation system (UCS), a major pathway for the degradation of cellular proteins in eukaroytic cells and in some bacteria. The UCS mediates the elimination of abnormal proteins and regulates the half-lives of important regulatory proteins that control cellular processes such as gene transcription and cell cycle progression. The UCS is implicated in the degradation of mitotic cyclin kinases, oncoproteins, tumor suppressor genes such as p53, viral proteins, cell surface receptors associated with signal transduction, transcriptional regulators, and mutated or damaged proteins (Ciechanover, supra).

[0008] Details of the cell division cycle may vary, but the basic process consists of three principle events. The first event, interphase, involves preparations for cell division, replication of the DNA, and production of essential proteins. In the second event, mitosis, the nuclear material is divided and separates to opposite sides of the cell. The final event, cytokinesis, is division and fission of the cell cytoplasm. The sequence and timing of cell cycle transitions is under the control of the cell cycle regulation system which controls the process by positive or negative regulatory circuits at various check points.

[0009] Mitosis marks the end of interphase and concludes with the onset of cytokinesis. There are four stages in mitosis, occurring in the following order: prophase, metaphase, anaphase and telophase. Prophase includes the formation of bi-polar mitotic spindles, composed of microtubules and associated proteins such as dynein, which originate from polar mitotic centers. During metaphase, the nuclear material condenses and develops kinetochore fibers which aid in its physical attachment to the mitotic spindles. The ensuing movement of the nuclear material to opposite poles along the mitotic spindles occurs during anaphase. Telophase includes the disappearance of the mitotic spindles and kinetochore fibers from the nuclear material. Mitosis depends on the interaction of numerous proteins. For example, centromere-associated proteins such as CENP-A, -B, and -C, play structural roles in kinetochore formation and assembly (Saffery, R. et al. (2000) Human Mol. Gen. 9: 175-185).

[0010] During the M phase of eukaryotic cell cycling, structural rearrangements occur ensuring appropriate distribution of cellular components between daughter cells. Breakdown of interphase structures into smaller subunits is common. The nuclear envelope breaks into vesicles, and nuclear lamins are disassembled. Subsequent phosphorylation of these lamins occurs and is maintained until telophase, at which time the nuclear lamina structure is reformed. cDNAs responsible for encoding M phase phosphorylation (MPPs) are components of U3 small nucleolar ribonucleoprotein (snoRNP), and relocalize to the nucleolus once mitosis is complete (Westendorf, J. M. et al. (1998) J. Biol. Chem. 9:437-449). U3 snoRNPs are essential mediators of RNA processing events.

[0011] Proteins involved in the regulation of cellular processes such as mitosis include the Ser/Thr-protein phosphatases type 1 (PP-1). PP-1s act by dephosphorylation of key proteins involved in the metaphase-anaphase transition. The gene PP1R7 encodes the regulatory polypeptide sds22, having at least six splice variants (Ceulemans, H. et al. (1999) Eur. J. Biochem. 262:36-42). Sds22 modulates the activity of the catalytic subunit of PP-1s, and enhances the PP-1-dependent dephosphorylation of mitotic substrates.

[0012] Cell cycle regulatory proteins play an important role in cell proliferation and cancer. For example, failures in the proper execution and timing of cell cycle events can lead to chromosome segregation defects resulting in aneuploidy or polyploidy. This genomic instability is characteristic of transformed cells (Luca, F. C. and Winey, M. (1998) Mol. Biol. Cell. 9:29-46). A recently identified protein, mMOB1, is the mammalian homolog of yeast MOB1, an essential yeast gene required for completion of mitosis and maintenance of ploidy. The mammalian mMOB1 is a member of protein complexes including protein phosphatase 2A (PP2A), and its phosphorylation appears to be regulated by PP2A (Moreno, C. S. et al. (2001) J. Biol. Chem. 276:24253-24260). PP2A has been implicated in the development of human cancers, including lung and colon cancers and leukemias.

[0013] Cell cycle regulation involves numerous proteins interacting in a sequential manner. The eukaryotic cell cycle consists of several highly controlled events whose precise order ensures successful DNA replication and cell division. Cells maintain the order of these events by making later events dependent on the successful completion of earlier events. This dependency is enforced by cellular mechanisms called checkpoints. Examples of additional cell cycle regulatory proteins include the histone deacetylases (HDACs). HDACs are involved in cell cycle regulation, and modulate chromatin structure. Human HDAC1 has been found to interact in vitro with the human Hus1 gene product, whose Schizosaccharomyces pombe homolog has been implicated in G₂/M checkpoint control (Cai, R. L. et al. (2000) J. Biol. Chem. 275:27909-27916).

[0014] DNA damage (G₂) and DNA replication (S-phase) checkpoints arrest eukaryotic cells at the G₂/M transition. This arrest provides time for DNA repair or DNA replication to occur before entry into mitosis. Thus, the G₂/M checkpoint ensures that mitosis only occurs upon completion of DNA replication and in the absence of chromosomal damage. The Hus1 gene of Schizosaccharomyces pombe is a cell cycle checkpoint gene, as are the rad family of genes (e.g., rad1 and rad9) (Volkmer, E. and Karnitz, L. M. (1999) J. Biol. Chem. 274:567-570; Kostrub C. F. et al. (1998) EMBO J. 17:2055-2066). These genes are involved in the mitotic checkpoint, and are induced by either DNA damage or blockage of replication. Induction of DNA damage or replication block leads to loss of function of the Hus1 gene and subsequent cell death. Human homologs have been identified for most of the rad genes, including ATM and ATR, the human homologs of rad3p. Mutations in the ATM gene are correlated with the severe congenital disease ataxia-telagiectasia (Savitsky, K. et al. (1995) Science 268:1749-1753). The human Hus1 protein has been shown to act in a complex with rad1 protein which interacts with rad9, making them central components of a DNA damage-responsive protein complex of human cells (Volkmer, E. and Karnitz, L. M. (1999) J. Biol. Chem. 274:567-570).

[0015] The entry and exit of a cell from mitosis is regulated by the synthesis and destruction of a family of activating proteins called cyclins. Cyclins act by binding to and activating a group of cyclin-dependent protein kinases (Cdks) which then phosphorylate and activate selected proteins involved in the mitotic process. Cyclins are characterized by a large region of shared homology that is approximately 180 amino acids in length and referred to as the “cyclin box” (Chapman, D. L. and Wolgemuth, D. J. (1993) Development 118:229-40). In addition, cyclins contain a conserved 9 amino acid sequence in the N-terminal region of the molecule called the “destruction box”. This sequence is believed to be a recognition code that triggers ubiquitin-mediated degradation of cyclin B (Hunt, T. (1991) Nature 349:100-101). Several types of cyclins exist (Ciechanover, A. (1994) Cell 79:13-21). Progression through G1 and S phase is driven by the G1 cyclins and their catalytic subunits, including Cdk2-cyclin A, Cdk2-cyclin E, Cdk4-cyclin D and Cdk6-cyclin D. Progression through the G2-M transition is driven by the activation of mitotic CDK-cyclin complexes such as Cdc2-cyclin A, Cdc2-cyclin B1 and Cdc2-cyclin B2 complexes (reviewed in Yang, J. and Kornbluth, S. (1999) Trends in Cell Biology 9:207-210).

[0016] Cyclins are degraded through the ubiquitin conjugation system (UCS), a major pathway for the degradation of cellular proteins in eukaroytic cells and in some bacteria. The UCS mediates the elimination of abnormal proteins and regulates the half-lives of important regulatory proteins that control cellular processes such as gene transcription and cell cycle progression. The UCS is implicated in the degradation of mitotic cyclin kinases, oncoproteins, tumor suppressor genes such as p53, viral proteins, cell surface receptors associated with signal transduction, transcriptional regulators, and mutated or damaged proteins (Ciechanover, supra).

[0017] The process of ubiquitin conjugation and protein degradation occurs in five principle steps (Jentsch, S. (1992) Annu. Rev. Genet. 26:179-207). First ubiquitin (Ub), a small, heat stable protein is activated by a ubiquitin-activating enzyme (E1) in an ATP dependent reaction which binds the C-terminus of Ub to the thiol group of an internal cysteine residue in E1. Second, activated Ub is transferred to one of several Ub-conjugating enzymes (E2). Different ubiquitin-dependent proteolytic pathways employ structurally similar, but distinct ubiquitin-conjugating enzymes that are associated with recognition subunits which direct them to proteins carrying a particular degradation signal. Third, E2 transfers the Ub molecule through its C-terminal glycine to a member of the ubiquitin-protein ligase family, E3. Fourth, E3 transfers the Ub molecule to the target protein. Additional Ub molecules may be added to the target protein forming a multi-Ub chain structure. Fifth, the ubiquinated protein is then recognized and degraded by the proteasome, a large, multisubunit proteolytic enzyme complex, and Ub is released for re-utilization.

[0018] Prior to activation, Ub is usually expressed as a fusion protein composed of an N-terminal ubiquitin and a C-terminal extension protein (CEP) or as a polyubiquitin protein with Ub monomers attached head to tail. CEPs have characteristics of a variety of regulatory proteins; most are highly basic, contain up to 30% lysine and arginine residues, and have nucleic acid-binding domains (Monia, B. P. et al. (1989) J. Biol. Chem. 264:4093-4103). The fusion protein is an important intermediate which appears to mediate co-regulation of the cell's translational and protein degradation activities, as well as localization of the inactive enzyme to specific cellular sites. Once delivered, C-terminal hydrolases cleave the fusion protein to release a functional Ub (Monia et al., supra).

[0019] Ub-conjugating enzymes (E2s) are important for substrate specificity in different UCS pathways. All E2s have a conserved domain of approximately 16 kDa called the UBC domain that is at least 35% identical in all E2s and contains a centrally located cysteine residue required for ubiquitin-enzyme thiolester formation (Jentsch, supra). A well conserved proline-rich element is located N-terminal to the active cysteine residue. Structural variations beyond this conserved domain are used to classify the E2 enzymes. Class I E2s consist almost exclusively of the conserved UBC domain. Class II E2s have various unrelated C-terminal extensions that contribute to substrate specificity and cellular localization. Class III E2s have unique N-terminal extensions which are believed to be involved in enzyme regulation or substrate specificity.

[0020] A mitotic cyclin-specific E2 (E2-C) is characterized by the conserved UBC domain, an N-terminal extension of 30 amino acids not found in other E2s, and a 7 amino acid unique sequence adjacent to this extension. These characteristics together with the high affinity of E2-C for cyclin identify it as a new class of E2 (Aristarkhov, A. et al. (1996) Proc. Natl. Acad. Sci. 93:4294-99).

[0021] Ubiquitin-protein ligases (E3s) catalyze the last step in the ubiquitin conjugation process, covalent attachment of ubiquitin to the substrate. E3 plays a key role in determining the specificity of the process. Only a few E3s have been identified so far. One type of E3 ligases is the HECT homologous to E6-AP C-terminus) domain protein family. One member of the family, E6-AP (E6-associated protein) is required, along with the human papillomavirus (HPV) E6 oncoprotein, for the ubiquitination and degradation of p53 (Scheffner et al. (1993) Cell 75:495-505). The C-terminal domain of HECT proteins contains the highly conserved ubiquitin-binding cysteine residue. The N-terminal region of the various HECT proteins is variable and is believed to be involved in specific substrate recognition (Huibregtse, J. M. et al. (1997) Proc. Natl. Acad. Sci. USA 94:3656-3661). The SCF (Skp1-Cdc53/Cullin-F box receptor) family of proteins comprise another group of ubiquitin ligases (Deshaies, R. (1999) Annu. Rev. Dev. Biol. 15:435-467). Multiple proteins are recruited into the SCF complex, including Skp1, cullin, and an F box domain containing protein. The F box protein binds the substrate for the ubiquitination reaction and may play roles in determining substrate specificity and orienting the substrate for reaction. Skp1 interacts with both the F box protein and cullin and may be involved in positioning the F box protein and cullin in the complex for transfer of ubiquitin from the E2 enzyme to the protein substrate. Substrates of SCF ligases include proteins involved in regulation of CDK activity, activation of transcription, signal transduction, assembly of kinetochores, and DNA replication.

[0022] Sgt1 was identified in a screen for genes in yeast that suppress defects in kinetochore function caused by mutations in Skp1 (Kitagawa, K. et al. (1999) Mol. Cell 4:21-33). Sgt1 interacts with Skp1 and associates with SCF ubiquitin ligase. Defects in Sgt1 cause arrest of cells at either G1 or G2 stages of the cell cycle. A yeast Sgt1 null mutant can be rescued by human Sgt1, an indication of the conservation of Sgt1 function across species. Sgt1 is required for assembly of kinetochore complexes in yeast.

[0023] Abnormal activities of the UCS are implicated in a number of diseases and disorders. These include, e.g., cachexia (Llovera, M. et al. (1995) Int. J. Cancer 61: 139-141), degradation of the tumor-suppressor protein, p53 (Ciechanover, supra), and neurodegeneration such as observed in Alzheimer's disease (Gregori, L. et al. (1994) Biochem. Biophys. Res. Commun. 203: 1731-1738). Since ubiquitin conjugation is a rate-limiting step in antigen presentation, the ubiquitin degradation pathway may also have a critical role in the immune response (Grant E. P. et al. (1995) J. Immunol. 155: 3750-3758).

[0024] Certain cell proliferation disorders can be identified by changes in the protein complexes that normally control progression through the cell cycle. A primary treatment strategy involves reestablishing control over cell cycle progression by manipulation of the proteins involved in cell cycle regulation (Nigg, E. A. (1995) BioEssays 17:471-480).

[0025] Tumor necrosis factor (TNF) and related cytokines induce apoptosis in lymphoid cells. (Reviewed in Nagata, S. (1997) Cell 88:355-365.) Binding of TNF to its receptor triggers a signal transduction pathway that results in the activation of a cascade of related proteases, called caspases. One such caspase, ICE (Interleukin-1β converting enzyme), is a cysteine protease comprised of two large and two small subunits generated by ICE auto-cleavage. (Dinarello, C. A. (1994) FASEB J. 8:1314-1325.) ICE is expressed primarily in monocytes. ICE processes the cytokine precursor, interleukin-1β, into its active form, which plays a central role in acute and chronic inflammation, bone resorption, myelogenous leukemia, and other pathological processes. ICE and related caspases cause apoptosis when overexpressed in transfected cell lines.

[0026] A final step in the apoptotic effector pathway is the fragmentation of nuclear DNA. Recently, a novel factor linking caspase activity to DNA fragmentation has been identified. (Xuesong, L. et al. (1997) Cell 89:175-184.) This factor, DNA fragmentation factor 45 (DFF-45), is proteolytically activated by caspase and is required for DNA fragmentation. DFF-45 is 331 amino acids in length and exists in the cell as a heterodimer with a second uncharacterized factor. The amino acid sequence of DFF-45 indicates that it is not a nuclease, suggesting that DFF-45 may activate a downstream nuclease. In addition, mRNA encoding a protein related to DFF-45 has been isolated from mouse adipogenic cells. (Danesch, U. et al. (1992) J. Biol. Chem. 267:7185-7193.) Expression of this mRNA is induced in steroid-treated, differentiating adipocytes. The predicted protein, FSP-27 (fat cell-specific, 27 kilodaltons), is highly basic with a predicted isoelectric point of 10.

[0027] Dysregulation of apoptosis has recently been recognized as a significant factor in the pathogenesis of many human diseases. For example, excessive cell survival caused by decreased apoptosis can contribute to disorders related to cell proliferation and the immune response. Such disorders include cancer, autoimmune diseases, viral infections, and inflammation. In contrast, excessive cell death caused by increased apoptosis can lead to degenerative and immunodeficiency disorders such as AIDS, neurodegenerative diseases, and myelodysplastic syndromes. (Thompson, C. B. (1995) Science 267:1456-1462.)

[0028] Embryogenesis

[0029] Mammalian embryogenesis is a process which encompasses the first few weeks of development following conception. During this period, embryogenesis proceeds from a single fertilized egg to the formation of the three embryonic tissues, then to an embryo which has most of its internal organs and all of its external features.

[0030] The normal course of mammalian embryogenesis depends on the correct temporal and spatial regulation of a large number of genes and tissues. These regulation processes have been intensely studied in mouse. An essential process that is still poorly understood is the activation of the embryonic genome after fertilization. As mouse oocytes grow, they accumulate transcripts that are either translated directly into proteins or stored for later activation by regulated polyadenylation. During subsequent meiotic maturation and ovulation, the maternal genome is transcriptionally inert, and most maternal transcripts are deadenylated and/or degraded prior to, or together with, the activation of the zygotic genes at the two-cell stage (Stutz, A. et al. (1998) Genes Dev. 12:2535-2548). The maternal to embryonic transition involves the degradation of oocyte, but not zygotic transcripts, the activation of the embryonic genome, and the induction of cell cycle progression to accommodate early development.

[0031] MATER (Maternal Antigen That Embryos Require) was initially identified as a target of antibodies from mice with ovarian immunity (Tong, Z-B., and Nelson, L. M. (1999) Endocrinology 140:3720-3726). Expression of the gene encoding MATER is restricted to the oocyte, making it one of a limited number of known maternal-effect genes in mammals (Tong, Z-B., et al. (2000) Mamm. Genome 11:281-287). The MATER protein is required for embryonic development beyond two cells, based upon preliminary results from mice in which this gene has been inactivated. The 1111-amino acid MATER protein contains a hydrophilic repeat region in the amino terminus, and a region containing 14 leucine-rich repeats in the carboxyl terminus. These repeats resemble the sequence found in porcine ribonuclease inhibitor that is critical for protein-protein interactions.

[0032] The degradation of maternal transcripts during meiotic maturation and ovulation may involve the activation of a ribonuclease just prior to ovulation. Thus the function of MATER may be to bind to the maternal ribonuclease and prevent degradation of zygotic transcripts (Tong (2000) supra). In addition to its role in oocyte development and embryogenesis, MATER may also be relevant to the pathogenesis of ovarian immunity, as it is a target of autoantibodies in mice with autoimmune oophoritis (Tong (1999) supra).

[0033] The maternal mRNA D7 is a moderately abundant transcript in Xenopus laevis whose expression is highest in, and perhaps restricted to, oogenesis and early embryogenesis. The D7 protein is absent from oocytes and first begins to accumulate during oocyte maturation. Its levels are highest during the first day of embryonic development and then they decrease. The loss of D7 protein affects the maturation process itself, significantly delaying the time course of germinal vesicle breakdown. Thus, D7 is a newly described protein involved in oocyte maturation (Smith R. C., et al. (1988) Genes Dev. 2(10):1296-306.)

[0034] Many other genes are involved in subsequent stages of embryogenesis. After fertilization, the oocyte is guided by fimbria at the distal end of each fallopian tube into and through the fallopian tube and thence into the uterus. Changes in the uterine endometrium prepare the tissue to support the implantation and embryonic development of a fertilized ovum. Several stages of division have occurred before the dividing ovum, now a blastocyst with about 100 cells, enters the uterus. Upon reaching the uterus, the developing blastocyst usually remains in the uterine cavity an additional two to four days before implanting in the endometrium, the inner lining of the uterus. Implantation results from the action of trophoblast cells that develop over the surface of the blastocyst. These cells secrete proteolytic enzymes that digest and liquefy the cells of the endometrium. The invasive process is reviewed in Fisher and Damsky (1993; Semin Cell Biol 4:183-188) and Graham and Lala (1992; Biochem Cell Biol 70:867-874). Once implantation has taken place, the trophoblast and other sublying cells proliferate rapidly, forming the placenta and the various membranes of pregnancy. (See Guyton, A. C. (1991) Textbook of Medical Physiology, 81′ ed. W. B. Saunders Company, Philadelphia pp. 915-919.)

[0035] The placenta has an essential role in protecting and nourishing the developing fetus. In most species the syncytiotrophoblast layer is present on the outside of the placenta at the fetal-maternal interface. This is a continuous structure, one cell deep, formed by the fusion of the constituent trophoblast cells. The syncytiotrophoblast cells play important roles in maternal-fetal exchange, in tissue remodeling during fetal development, and in protecting the developing fetus from the maternal immune response (Stoye, J. P. and Coffin, J. M. (2000) Nature 403:715-717).

[0036] A gene called syncytin is the envelope gene of a human endogenous defective provirus. Syncytin is expressed in high levels in placenta, and more weakly in testis, but is not detected in any other tissues (Mi, S. et al. (2000) Nature 403:785-789). Syncytin expression in the placenta is restricted to the syncytiotrophoblasts. Since retroviral env proteins are often involved in promoting cell fusion events, it was thought that syncytin might be involved in regulating the fusion of trophoblast cells into the syncytiotrophoblast layer. Experiments demonstrated that syncytin can mediate cell fusion in vitro, and that anti-syncytin antibodies can inhibit the fusion of placental cytotrophoblasts (Mi, supra). In addition, a conserved immunosuppressive domain present in retroviral envelope proteins, and found in syncytin at amino acid residues 373-397, might be involved in preventing maternal immune responses against the developing embryo.

[0037] Syncytin may also be involved in regulating trophoblast invasiveness by inducing trophoblast fusion and terminal differentiation (Mi, supra). Insufficient trophoblast infiltration of the uterine wall is associated with placental disorders such as preeclampsia, or pregnancy induced hypertension, while uncontrolled trophoblast invasion is observed in choriocarcinoma and other gestational trophoblastic diseases. Thus syncytin function may be involved in these diseases.

[0038] Cell Division

[0039] Cell division is the fundamental process by which all living things grow and reproduce. In unicellular organisms such as yeast and bacteria, each cell division doubles the number of organisms, while in multicellular species many rounds of cell division are required to replace cells lost by wear or by programmed cell death, and for cell differentiation to produce a new tissue or organ. Details of the cell division cycle may vary, but the basic process consists of three principle events. The first event, interphase, involves preparations for cell division, replication of the DNA, and production of essential proteins. In the second event, mitosis, the nuclear material is divided and separates to opposite sides of the cell. The final event, cytokinesis, is division and fission of the cell cytoplasm. The sequence and timing of cell cycle transitions is under the control of the cell cycle regulation system which controls the process by positive or negative regulatory circuits at various check points.

[0040] Regulated progression of the cell cycle depends on the integration of growth control pathways with the basic cell cycle machinery. Cell cycle regulators have been identified by selecting for human and yeast cDNAs that block or activate cell cycle arrest signals in the yeast mating pheromone pathway when they are overexpressed. Known regulators include human CPR (cell cycle progression restoration) genes, such as CPR8 and CPR2, and yeast CDC (cell division control) genes, including CDC91, that block the arrest signals. The CPR genes express a variety of proteins including cyclins, tumor suppressor binding proteins, chaperones, transcription factors, translation factors, and RNA-binding proteins (Edwards, M. C. et al. (1997) Genetics 147:1063-1076).

[0041] Several cell cycle transitions, including the entry and exit of a cell from mitosis, are dependent upon the activation and inhibition of cyclin-dependent kinases (Cdks). The Cdks are composed of a kinase subunit, Cdk, and an activating subunit, cyclin, in a complex that is subject to many levels of regulation. There appears to be a single Cdk in Saccharomyces cerevisiae and Saccharomyces pombe whereas mammals have a variety of specialized Cdks. Cyclins act by binding to and activating cyclin-dependent protein kinases which then phosphorylate and activate selected proteins involved in the mitotic process. The Cdk-cyclin complex is both positively and negatively regulated by phosphorylation, and by targeted degradation involving molecules such as CDC4 and CDC53. In addition, Cdks are further regulated by binding to inhibitors and other proteins such as Suc1 that modify their specificity or accessibility to regulators (Patra, D. and W. G. Dunphy (1996) Genes Dev. 10:1503-1515; and Mathias, N. et al. (1996) Mol. Cell Biol. 16:6634-6643).

[0042] Reproduction

[0043] The male and female reproductive systems are complex and involve many aspects of growth and development. The anatomy and physiology of the male and female reproductive systems are reviewed in (Guyton, A. C. (1991) Textbook of Medical Physiology, W. B. Saunders Co., Philadelphia Pa., pp. 899-928).

[0044] The male reproductive system includes the process of spermatogenesis, in which the sperm are formed, and male reproductive functions are regulated by various hormones and their effects on accessory sexual organs, cellular metabolism, growth, and other bodily functions.

[0045] Spermatogenesis begins at puberty as a result of stimulation by gonadotropic hormones released from the anterior pituitary. Immature sperm (spermatogonia) undergo several mitotic cell divisions before undergoing meiosis and full maturation. The testes secrete several male sex hormones, the most abundant being testosterone, that is essential for growth and division of the immature sperm, and for the masculine characteristics of the male body. Three other male sex hormones, gonadotropin-releasing hormone (GnRH), luteinizing hormone (LH), and follicle-stimulating hormone (FSH) control sexual function.

[0046] The uterus, ovaries, fallopian tubes, vagina, and breasts comprise the female reproductive system. The ovaries and uterus are the source of ova and the location of fetal development, respectively. The fallopian tubes and vagina are accessory organs attached to the top and bottom of the uterus, respectively. Both the uterus and ovaries have additional roles in the development and loss of reproductive capability during a female's lifetime. The primary role of the breasts is lactation. Multiple endocrine signals from the ovaries, uterus, pituitary, hypothalamus, adrenal glands, and other tissues coordinate reproduction and lactation. These signals vary during the monthly menstruation cycle and during the female's lifetime. Similarly, the sensitivity of reproductive organs to these endocrine signals varies during the female's lifetime.

[0047] A combination of positive and negative feedback to the ovaries, pituitary and hypothalamus glands controls physiologic changes during the monthly ovulation and endometrial cycles. The anterior pituitary secretes two major gonadotropin hormones, follicle-stimulating hormone (FSH) and luteinizing hormone (LH), regulated by negative feedback of steroids, most notably by ovarian estradiol. If fertilization does not occur, estrogen and progesterone levels decrease. This sudden reduction of the ovarian hormones leads to menstruation, the desquamation of the endometrium.

[0048] Hormones further govern all the steps of pregnancy, parturition, lactation, and menopause. During pregnancy large quantities of human chorionic gonadotropin (hCG), estrogens, progesterone, and human chorionic somatomammotropin (hCS) are formed by the placenta. hCG, a glycoprotein similar to luteinizing hormone, stimulates the corpus luteum to continue producing more progesterone and estrogens, rather than to involute as occurs if the ovum is not fertilized. hCS is similar to growth hormone and is crucial for fetal nutrition.

[0049] The female breast also matures during pregnancy. Large amounts of estrogen secreted by the placenta trigger growth and branching of the breast milk ductal system while lactation is initiated by the secretion of prolactin by the pituitary gland.

[0050] Parturition involves several hormonal changes that increase uterine contractility toward the end of pregnancy, as follows. The levels of estrogens increase more than those of progesterone. Oxytocin is secreted by the neurohypophysis. Concomitantly, uterine sensitivity to oxytocin increases. The fetus itself secretes oxytocin, cortisol (from adrenal glands), and prostaglandins.

[0051] Menopause occurs when most of the ovarian follicles have degenerated. The ovary then produces less estradiol, reducing the negative feedback on the pituitary and hypothalamus glands. Mean levels of circulating FSH and LH increase, even as ovulatory cycles continue. Therefore, the ovary is less responsive to gonadotropins, and there is an increase in the time between menstrual cycles. Consequently, menstrual bleeding ceases and reproductive capability ends.

[0052] Cell Differentiation and Proliferation

[0053] Tissue growth involves complex and ordered patterns of cell proliferation, cell differentiation, and apoptosis. Cell proliferation must be regulated to maintain both the number of cells and their spatial organization. This regulation depends upon the appropriate expression of proteins which control cell cycle progression in response to extracellular signals, such as growth factors and other mitogens, and intracellular cues, such as DNA damage or nutrient starvation. Molecules which directly or indirectly modulate cell cycle progression fall into several categories, including growth factors and their receptors, second messenger and signal transduction proteins, oncogene products, tumor-suppressor proteins, and mitosis-promoting factors.

[0054] Growth factors were originally described as serum factors required to promote cell proliferation. Most growth factors are large, secreted polypeptides that act on cells in their local environment. Growth factors bind to and activate specific cell surface receptors and initiate intracellular signal transduction cascades. Many growth factor receptors are classified as receptor tyrosine kinases which undergo autophosphorylation upon ligand binding. Autophosphorylation enables the receptor to interact with signal transduction proteins characterized by the presence of SH2 or SH3 domains (Src homology regions 2 or 3). These proteins then modulate the activity state of small G-proteins, such as Ras, Rab, and Rho, along with GTPase activating proteins (GAPs), guanine nucleotide releasing proteins (GNRPs), and other guanine nucleotide exchange factors. Small G proteins act as molecular switches that activate other downstream events, such as mitogen-activated protein kinase (MAP kinase) cascades. MAP kinases ultimately activate transcription of mitosis-promoting genes.

[0055] In addition to growth factors, small signaling peptides and hormones also influence cell proliferation. These molecules bind primarily to another class of receptor, the trimeric G-protein coupled receptor (GPCR), found predominantly on the surface of immune, neuronal and neuroendocrine cells. Upon ligand binding, the GPCR activates a trimeric G protein which in turn triggers increased levels of intracellular second messengers such as phospholipase C, Ca2+, and cyclic AMP. Most GPCR-mediated signaling pathways indirectly promote cell proliferation by causing the secretion or breakdown of other signaling molecules that have direct mitogenic effects. These signaling cascades often involve activation of kinases and phosphatases. Some growth factors, such as some members of the transforming growth factor beta (TGF-β) family, act on some cells to stimulate cell proliferation and on other cells to inhibit it. Growth factors may also stimulate a cell at one concentration and inhibit the same cell at another concentration. Most growth factors also have a multitude of other actions besides the regulation of cell growth and division: they can control the proliferation, survival, differentiation, migration, or function of cells depending on the circumstance. For example, the tumor necrosis factor/nerve growth factor (TNF/NGF) family can activate or inhibit cell death, as well as regulate proliferation and differentiation. The cell response depends on the type of cell, its stage of differentiation and transformation status, which surface receptors are stimulated, and the types of stimuli acting on the cell (Smith, A. et al. (1994) Cell 76:959-962; and Nocentini, G. et al. (1997) Proc. Natl. Acad. Sci. USA 94:6216-6221).

[0056] Neighboring cells in a tissue compete for growth factors, and when provided with “unlimited” quantities in a perfused system will grow to even higher cell densities before reaching density-dependent inhibition of cell division. Cells often demonstrate an anchorage dependence of cell division as well. This anchorage dependence may be associated with the formation of focal contacts linking the cytoskeleton with the extracellular matrix (ECM). The expression of ECM components can be stimulated by growth factors. For example, TGF-β stimulates fibroblasts to produce a variety of ECM proteins, including fibronectin, collagen, and tenascin (Pearson, C. A. et al. (1988) EMBO J. 7:2677-2981). In fact, for some cell types specific ECM molecules, such as laminin or fibronectin, may act as growth factors. Tenascin-C and -R, expressed in developing and lesioned neural tissue, provide stimulatory/anti-adhesive or inhibitory properties, respectively, for axonal growth (Faissner, A. (1997) Cell Tissue Res. 290:331-341).

[0057] Cancers are associated with the activation of oncogenes which are derived from normal cellular genes. These oncogenes encode oncoproteins which convert normal cells into malignant cells. Some oncoproteins are mutant isoforms of the normal protein, and other oncoproteins are abnormally expressed with respect to location or amount of expression. The latter category of oncoprotein causes cancer by altering transcriptional control of cell proliferation. Five classes of oncoproteins are known to affect cell cycle controls. These classes include growth factors, growth factor receptors, intracellular signal transducers, nuclear transcription factors, and cell-cycle control proteins. Viral oncogenes are integrated into the human genome after infection of human cells by certain viruses. Examples of viral oncogenes include v-src, v-abl, and v-fps. Many cases related to the overexpression of proteins associated with tumors and metastasis have been reported. The Mta1 gene has been cloned in mice, in both cell lines and tissues representing metastatic tumors (Simpson, A. et al. (2001) Gene 273:29-39). Expression of the melanoma antigen-encoding gene (MAGE) family of proteins has also been detected in many tumors. GAC1, a new member of the leucine-rich repeat superfamily, is amplified and overexpressed in malignant gliomas (Almeida, A. et al. (1998) Oncogene 16:2997-3002).

[0058] Many oncogenes have been identified and characterized. These include sis, erbA, erbB, her-2, mutated G_(s), src, abl, ras, crk, jun, fos, myc, and mutated tumor-suppressor genes such as RB, p53, mdm2, Cip1, p16, and cyclin D. Transformation of normal genes to oncogenes may also occur by chromosomal translocation. The Philadelphia chromosome, characteristic of chronic myeloid leukemia and a subset of acute lymphoblastic leukemias, results from a reciprocal translocation between chromosomes 9 and 22 that moves a truncated portion of the proto-oncogene c-abl to the breakpoint cluster region (bcr) on chromosome 22.

[0059] Tumor-suppressor genes are involved in regulating cell proliferation. Mutations which cause reduced or loss of function in tumor-suppressor genes result in uncontrolled cell proliferation. For example, the retinoblastoma gene product (RB), in a non-phosphorylated state, binds several early-response genes and suppresses their transcription, thus blocking cell division. Phosphorylation of RB causes it to dissociate from the genes, releasing the suppression, and allowing cell division to proceed.

[0060] SEB (SET-binding protein) is a novel nuclear protein that interacts in a yeast two-hybrid system and in human cells with SET, the translocation breakpoint-encoded protein in acute undifferentiated leukemia. SEB also has an oncoprotein Ski homologous region, six PEST suquences and three sequential PPLPPPPP repeats at the C-terminus. SEB mRNA is expressed ubiquitously in all examined human adult tissues and cells. SET has been mapped to chromosome 18q21.1. This reagon also contains tumor suppressor genes associated with deletions in cancer and leukemia (Minakuchi, M. et al. (2001) Eru. J. Biochem. 268:1340-1351).

[0061] Cell Differentiation

[0062] Multicellular organisms are comprised of diverse cell types that differ dramatically both in structure and function, despite the fact that each cell is like the others in its hereditary endowment. Cell differentiation is the process by which cells come to differ in their structure and physiological function. The cells of a multicellular organism all arise from mitotic divisions of a single-celled zygote. The zygote is totipotent, meaning that it has the ability to give rise to every type of cell in the adult body. During development the cellular descendants of the zygote lose their totipotency and become determined. Once its prospective fate is achieved, a cell is said to have differentiated. All descendants of this cell will be of the same type.

[0063] Human growth and development requires the spatial and temporal regulation of cell differentiation, along with cell proliferation and regulated cell death. These processes coordinate to control reproduction, aging, embryogenesis, morphogenesis, organogenesis, and tissue repair and maintenance. The processes involved in cell differentiation are also relevant to disease states such as cancer, in which case the factors regulating normal cell differentiation have been altered, allowing the cancerous cells to proliferate in an anaplastic, or undifferentiated, state.

[0064] The mechanisms of differentiation involve cell-specific regulation of transcription and translation, so that different genes are selectively expressed at different times in different cells. Genetic experiments using the fruit fly Drosophila melanogaster have identified regulated cascades of transcription factors which control pattern formation during development and differentiation. These include the homeotic genes, which encode transcription factors containing homeobox motifs. The products of homeotic genes determine how the insect's imaginal discs develop from masses of undifferentiated cells to specific segments containing complex organs. Many genes found to be involved in cell differentiation and development in Drosophila have homologs in mammals. Some human genes have equivalent developmental roles to their Drosophila homologs. The human homolog of the Drosophila eyes absent gene (eya) underlies branchio-oto-renal syndrome, a developmental disorder affecting the ears and kidneys (Abdelhak, S. et al. (1997) Nat. Genet. 15:157-164). The Drosophila slit gene encodes a secreted leucine-rich repeat containing protein expressed by the midline glial cells and required for normal neural development.

[0065] At the cellular level, growth and development are governed by the cell's decision to enter into or exit from the cell cycle and by the cell's commitment to a terminally differentiated state. Differential gene expression within cells is triggered in response to extracellular signals and other environmental cues. Such signals include growth factors and other nitrogens such as retinoic acid; cell-cell and cell-matrix contacts; and environmental factors such as nutritional signals, toxic substances, and heat shock. Candidate genes that may play a role in differentiation can be identified by altered expression patterns upon induction of cell differentiation in vitro.

[0066] The final step in cell differentiation results in a specialization that is characterized by the production of particular proteins, such as contractile proteins in muscle cells, serum proteins in liver cells and globins in red blood cell precursors. The expression of these specialized proteins depends at least in part on cell-specific transcription factors. For example, the homobox-containing transcription factor PAX-6 is essential for early eye determination, specification of ocular tissues, and normal eye development in vertebrates.

[0067] In the case of epidermal differentiation, the induction of differentiation-specific genes occurs either together with or following growth arrest and is believed to be linked to the molecular events that control irreversible growth arrest. Irreversible growth arrest is an early event which occurs when cells transit from the basal to the innermost suprabasal layer of the skin and begin expressing squamous-specific genes. These genes include those involved in the formation of the cross-linked envelope, such as transglutaminase I and III, involucrin, loricin, and small proline-rich repeat (SPRR) proteins. The SPRR proteins are 8-10 kDa in molecular mass, rich in proline, glutamine, and cysteine, and contain similar repeating sequence elements. The SPRR proteins may be structural proteins with a strong secondary structure or metal-binding proteins such as metallothioneins. (Jetten, A. M. and Harvat, B. L. (1997) J. Dermatol. 24:711-725; PRINTS Entry PR00021 PRORICH Small proline-rich protein signature.)

[0068] The Wnt gene family of secreted signaling molecules is highly conserved throughout eukaryotic cells. Members of the Wnt family are involved in regulating chondrocyte differentiation within the cartilage template. Wnt-5a, Wnt-5b and Wnt-4 genes are expressed in chondrogenic regions of the chicken limb, Wnt-5a being expressed in the perichondrium (mesenchymal cells immediately surrounding the early cartilage template). Wnt-5a misexpression delays the maturation of chondrocytes and the onset of bone collar formation in chicken limb (Hartmann, C. and Tabin, C. J. (2000) Development 127:3141-3159).

[0069] Glypicans are a family of cell surface heparan sulfate proteoglycans that play an important role in cellular growth control and differentiation. Cerebroglycan, a heparan sulfate proteoglycan expressed in the nervous system, is involved with the motile behavior of developing neurons (Stipp, C. S. et al. (1994) J. Cell Biol. 124:149-160).

[0070] Notch plays an active role in the differentiation of glial cells, and influences the length and organization of neuronal processes (for a review, see Frisen, J. and Lendahl, U. (2001) Bioessays 23:3-7). The Notch receptor signaling pathway is important for morphogenesis and development of many organs and tissues in multicellular species. Drosophila fringe proteins modulate the activation of the Notch signal transduction pathway at the dorsal-ventral boundary of the wing imaginal disc. Mammalian fringe-related family members participate in boundary determination during segmentation (Johnston, S. H. et al. (1997) Development 124:2245-2254).

[0071] Recently a number of proteins have been found to contain a conserved cysteine-rich domain of about 60 amino-acid residues called the LIM domain (for Lin-11 Isl-1 Mec-3) (Freyd G. et al. (1990) Nature 344:876-879; Baltz R. et al. (1992) Plant Cell 4:1465-1466). In the LIM domain, there are seven conserved cysteine residues and a histidine. The LIM domain binds two zinc ions (Michelsen J. W. et al. (1993) Proc. Natl. Acad. Sci. U.S.A. 90:4404-4408). LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction.

[0072] Apoptosis

[0073] Normal development, growth, and homeostasis in multicellular organisms require a careful balance between the production and destruction of cells in tissues throughout the body. Cell division is a carefully coordinated process with numerous checkpoints and control mechanisms. These mechanisms are designed to regulate DNA replication and to prevent inappropriate or excessive cell proliferation. In contrast, apoptosis is the genetically controlled process by which unneeded or defective cells undergo programmed cell death. Unlike necrotic or injured cells, apoptotic cells are rapidly phagocytosed by neighboring cells or macrophages without leaking their potentially damaging contents into the surrounding tissue or triggering an inflammatory response.

[0074] Apoptosis is the genetically controlled process by which unneeded or defective cells undergo programmed cell death. Selective elimination of cells is as important for morphogenesis and tissue remodeling as is cell proliferation and differentiation. Lack of apoptosis may result in hyperplasia and other disorders associated with increased cell proliferation. Apoptosis is also a critical component of the immune response. Immune cells such as cytotoxic T-cells and natural killer cells prevent the spread of disease by inducing apoptosis in tumor cells and virus-infected cells. In addition, immune cells that fail to distinguish self molecules from foreign molecules must be eliminated by apoptosis to avoid an autoimmune response.

[0075] Apoptotic cells undergo distinct morphological changes. Hallmarks of apoptosis include cell shrinkage, nuclear and cytoplasmic condensation, and alterations in plasma membrane topology. Biochemically, apoptotic cells are characterized by increased intracellular calcium concentration, fragmentation of chromosomal DNA, and expression of novel cell surface components.

[0076] The molecular mechanisms of apoptosis are highly conserved, and many of the key protein regulators and effectors of apoptosis have been identified. Apoptosis generally proceeds in response to a signal which is transduced intracellularly and results in altered patterns of gene expression and protein activity. Signaling molecules such as hormones and cytokines are known both to stimulate and to inhibit apoptosis through interactions with cell surface receptors. Transcription factors also play an important role in the onset of apoptosis. A number of downstream effector molecules, especially proteases, have been implicated in the degradation of cellular components and the proteolytic activation of other apoptotic effectors.

[0077] The Bcl-2 family of proteins, as well as other cytoplasmic proteins, are key regulators of apoptosis. There are at least 15 Bcl-2 family members within 3 subfamilies. These proteins have been identified in mammalian cells and in viruses, and each possesses at least one of four Bcl-2 homology domains (BH1 to BH4), which are highly conserved. Bcl-2 family proteins contain the BH1 and BH2 domains, which are found in members of the pro-survival subfamily, while those proteins which are most similar to Bcl-2 have all four conserved domains, enabling inhibition of apoptosis following encounters with a variety of cytotoxic challenges. Members of the pro-survival subfamily include Bcl-2, Bcl-x_(L), Bcl-w, Mcl-1, and A1 in mammals; NF-13 (chicken); CED-9 (Caenorhabditis elegans); and viral proteins BHRF1, LMW5-HL, ORF16, KS-Bcl-2, and E1B-19K. The BH3 domain is essential for the function of pro-apoptosis subfamily proteins. The two pro-apoptosis subfamilies, Bax and BH3, include Bax, Bak, and Bok (also called Mtd); and Bik, Blk, Hrk, BNIP3, Bim_(L), Bad, Bid, and Egl-1 (C. elegans); respectively. Members of the Bax subfamily contain the BH1, BH2, and BH3 domains, and resemble Bcl-2 rather closely. In contrast, members of the BH3 subfamily have only the 9-16 residue BH3 domain, being otherwise unrelated to any known protein, and only Bik and Blk share sequence similarity. The proteins of the two pro-apoptosis subfamilies may be the antagonists of pro-survival subfamily proteins. This is illustrated in C. elegans where Egl-1, which is required for apoptosis, binds to and acts via CED-9 (for review, see Adams, J. M. and Cory, S. (1998) Science 281:1322-1326).

[0078] Heterodimerization between pro-apoptosis and anti-apoptosis subfamily proteins seems to have a titrating effect on the functions of these protein subfamilies, which suggests that relative concentrations of the members of each subfamily may act to regulate apoptosis. Heterodimerization is not required for a pro-survival protein; however, it is essential in the BH3 subfamily, and less so in the Bax subfamily.

[0079] The Bcl-2 protein has 2 isoforms, alpha and beta, which are formed by alternative splicing. It forms homodimers and heterodimers with Bax and Bak proteins and the Bcl-X isoform Bcl-x_(S). Heterodimerization with Bax requires intact BH1 and BH2 domains, and is necessary for pro-survival activity. The BH4 domain seems to be involved in pro-survival activity as well. Bcl-2 is located within the inner and outer mitochondrial membranes, as well as within the nuclear envelope and endoplasmic reticulum, and is expressed in a variety of tissues. Its involvement in follicular lymphoma (type II chronic lymphatic leukemia) is seen in a chromosomal translocation T(14;18)(q32;q21) and involves immunoglobulin gene regions.

[0080] The Bcl-x protein is a dominant regulator of apoptotic cell death. Alternative splicing results in three isoforms, Bcl-xB, a long isoform, and a short isoform. The long isoform exhibits cell death repressor activity, while the short isoform promotes apoptosis. Bcl-xL forms heterodimers with Bax and Bak, although heterodimerization with Bax does not seem to be necessary for pro-survival (anti-apoptosis) activity. Bcl-xS forms heterodimers with Bcl-2. Bcl-x is found in mitochondrial membranes and the perinuclear envelope. Bcl-xS is expressed at high levels in developing lymphocytes and other cells undergoing a high rate of turnover. Bcl-xL is found in adult brain and in other tissues' long-lived post-mitotic cells. As with Bcl-2, the BH1, BH2, and BH4 domains are involved in pro-survival activity.

[0081] The Bcl-w protein is found within the cytoplasm of almost all myeloid cell lines and in numerous tissues, with the highest levels of expression in brain, colon, and salivary gland. This protein is expressed in low levels in testis, liver, heart, stomach, skeletal muscle, and placenta, and a few lymphoid cell lines. Bcl-w contains the BH1, BH2, and BH4 domains, all of which are needed for its cell survival promotion activity. Although mice in which Bcl-w gene function was disrupted by homologous recombination were viable, healthy, and normal in appearance, and adult females had normal reproductive function, the adult males were infertile. In these males, the initial, prepuberty stage of spermatogenesis was largely unaffected and the testes developed normally. However, the seminiferous tubules were disorganized, contained numerous apoptotic cells, and were incapable of producing mature sperm. This mouse model may be applicable to some cases of human male sterility and suggests that alteration of programmed cell death in the testes may be useful in modulating fertility (Print, C. G. et al. (1998) Proc. Natl. Acad. Sci. USA 95:12424-12431).

[0082] Studies in rat ischemic brain found Bcl-w to be overexpressed relative to its normal low constitutive level of expression in nonischemic brain. Furthermore, in vitro studies to examine the mechanism of action of Bcl-w revealed that isolated rat brain mitochondria were unable to respond to an addition of recombinant Bax or high concentrations of calcium when Bcl-w was also present. The normal response would be the release of cytochrome c from the mitochondria. Additionally, recombinant Bcl-w protein was found to inhibit calcium-induced loss of mitochondrial transmembrane potential, which is indicative of permeability transition. Together these findings suggest that Bcl-w may be a neuro-protectant against ischemic neuronal death and may achieve this protection via the mitochondrial death-regulatory pathway (Yan, C. et al. (2000) J. Cereb. Blood Flow Metab. 20:620-630).

[0083] The bfl-1 gene is an additional member of the Bcl-2 family, and is also a suppressor of apoptosis. The Bfl-1 protein has 175 amino acids, and contains the BH1, BH2, and BH3 conserved domains found in Bcl-2 family members. It also contains a Gln-rich NH-terminal region and lacks an NH domain 1, unlike other Bcl-2 family members. The mouse A1 protein shares high sequence homology with Bfl-1 and has the 3 conserved domains found in Bfl-1. Apoptosis induced by the p53 tumor suppressor protein is suppressed by Bfl-1, similar to the action of Bcl-2, Bcl-xL, and EBV-BHRF1 (D'Sa-Eipper, C. et al. (1996) Cancer Res. 56:3879-3882). Bfl-1 is found intracellularly, with the highest expression in the hematopoietic compartment, i.e. blood, spleen, and bone marrow; moderate expression in lung, small intestine, and testis; and minimal expression in other tissues. It is also found in vascular smooth muscle cells and hematopoietic malignancies. A correlation has been noted between the expression level of bfl-1 and the development of stomach cancer, suggesting that the Bfl-1 protein is involved in the development of stomach cancer, either in the promotion of cancerous cell survival or in cancer (Choi, S. S. et al. (1995) Oncogene 11:1693-1698).

[0084] Cancers are characterized by continuous or uncontrolled cell proliferation. Some cancers are associated with suppression of normal apoptotic cell death. Strategies for treatment may involve either reestablishing control over cell cycle progression, or selectively stimulating apoptosis in cancerous cells (Nigg, E. A. (1995) BioEssays 17:471-480). Immunological defenses against cancer include induction of apoptosis in mutant cells by tumor suppressors, and the recognition of tumor antigens by T lymphocytes. Response to mitogenic stresses is frequently controlled at the level of transcription and is coordinated by various transcription factors. For example, the Rel/NF-kappa B family of vertebrate transcription factors plays a pivotal role in inflammatory and immune responses to radiation. The NF-kappa B family includes p50, p52, RelA, RelB, cRel, and other DNA-binding proteins. The p52 protein induces apoptosis, upregulates the transcription factor c-Jun, and activates c-Jun N-terminal kinase 1 (JNK1) (Sun, L. et al. (1998) Gene 208:157-166). Most NF-kappa B proteins form DNA-binding homodimers or heterodimers. Dimerization of many transcription factors is mediated by a conserved sequence known as the bZIP domain, characterized by a basic region followed by a leucine zipper.

[0085] The Fas/Apo-1 receptor (FAS) is a member of the tumor necrosis factor (TNF) receptor family. Upon binding its ligand (Fas ligand), the membrane-spanning FAS induces apoptosis by recruiting several cytoplasmic proteins that transmit the death signal. One such protein, termed FAS-associated protein factor 1 (FAF1), was isolated from mice, and it was demonstrated that expression: of FAF1 in L cells potentiated FAS-induced apoptosis (Chu, K. et al. (1995) Proc. Natl. Acad. Sci. USA 92:11894-11898). Subsequently, FAS-associated factors have been isolated from numerous other species, including fruit fly and quail (Frohlich, T. et al. (1998) J. Cell Sci. 111:2353-2363). Another cytoplasmic protein that functions in the transmittal of the death signal from Fas is the Fas-associated death domain protein, also known as FADD. FADD transmits the death signal in both FAS-mediated and TNF receptor-mediated apoptotic pathways by activating caspase-8 (Bang, S. et al. (2000) J. Biol. Chem. 275:36217-36222).

[0086] Fragmentation of chromosomal DNA is one of the hallmarks of apoptosis. DNA fragmentation factor (DFF) is a protein composed of two subunits, a 40-kDa caspase-activated nuclease termed DFF40/CAD, and its 45-kDa inhibitor DFF45/ICAD. Two mouse homologs of DFF45/ICAD, termed CIDE-A and CIDE-B, have recently been described (Inohara, N. et al. (1998) EMBO J. 17:2526-2533). CIDE-A and CIDE-B expression in mammalian cells activated apoptosis, while expression of CIDE-A alone induced DNA fragmentation. In addition, FAS-mediated apoptosis was enhanced by CIDE-A and CIDE-B, further implicating these proteins as effectors that mediate apoptosis.

[0087] Transcription factors play an important role in the onset of apoptosis. A number of downstream effector molecules, particularly proteases such as the cysteine proteases called caspases, are involved in the initiation and execution phases of apoptosis. The activation of the caspases results from the competitive action of the pro-survival and pro-apoptosis Bcl-2-related proteins (Print, C. G. et al. (1998) Proc. Natl. Acad. Sci. USA 95:12424-12431). A pro-apoptotic signal can activate initiator caspases that trigger a proteolytic caspase cascade, leading to the hydrolysis of target proteins and the classic apoptotic death of the cell. Two active site residues, a cysteine and a histidine, have been implicated in the catalytic mechanism. Caspases are among the most specific endopeptidases, cleaving after aspartate residues.

[0088] Caspases are synthesized as inactive zymogens consisting of one large (p20) and one small (p10) subunit separated by a small spacer region, and a variable N-terminal prodomain. This prodomain interacts with cofactors that can positively or negatively affect apoptosis. An activating signal causes autoproteolytic cleavage of a specific aspartate residue (D297 in the caspase-1 numbering convention) and removal of the spacer and prodomain, leaving a p10/p20 heterodimer. Two of these heterodimers interact via their small subunits to form the catalytically active tetramer. The long prodomains of some caspase family members have been shown to promote dimerization and auto-processing of procaspases. Some caspases contain a “death effector domain” in their prodomain by which they can be recruited into self-activating complexes with other caspases and FADD protein-associated death receptors or the TNF receptor complex. In addition, two dimers from different caspase family members can associate, changing the substrate specificity of the resultant tetramer.

[0089] Impaired regulation of apoptosis is associated with loss of neurons in Alzheimer's disease. Alzheimer's disease is a progressive neurodegenerative disorder that is characterized by the formation of senile plaques and neurofibrillary tangles containing amyloid beta peptide. These plaques are found in limbic and association cortices of the brain, including hippocampus, temporal cortices, cingulate cortex, amygdala, nucleus basalis and locus caeruleus. B-amyloid peptide participates in signaling pathways that induce apoptosis and lead to the death of neurons. (Kajkowski, C. et al. (2001) J. Biol. Chem. 276:18748-18756). Early in Alzheimer's pathology, physiological changes are visible in the cingulate cortex (Minoshima, S. et al. (1997) Annals of Neurology 42:85-94). In subjects with advanced Alzheimer's disease, accumulating plaques damage the neuronal architecture in limbic areas and eventually cripple the memory process.

[0090] Tumor necrosis factor (TNF) and related cytokines induce apoptosis in lymphoid cells. (Reviewed in Nagata, S. (1997) Cell 88:355-365.) Binding of TNF to its receptor triggers a signal transduction pathway that results in the activation of a proteolytic caspase cascade. One such caspase, ICE (Interleukin-1β converting enzyme), is a cysteine protease comprised of two large and two small subunits generated by ICE auto-cleavage (Dinarello, C. A. (1994) FASEB J. 8:1314-1325). ICE is expressed primarily in monocytes. ICE processes the cytokine precursor, interleukin-1β, into its active form, which plays a central role in acute and chronic inflammation, bone resorption, myelogenous leukemia, and other pathological processes. ICE and related caspases cause apoptosis when overexpressed in transfected cell lines.

[0091] A caspase recruitment domain (CARD) is found within the prodomain of several apical caspases and is conserved in several apoptosis regulatory molecules such as Apaf-2, RAIDD, and cellular inhibitors of apoptosis proteins (IAPs) (Hofmann, K. et al. (1997) Trends Biochem. Sci. 22:155-157). The regulatory role of CARD in apoptosis may be to allow proteins such as Apaf-1 to associate with caspase-9 (Li, P. et al. (1997) Cell 91:479-489). A human cDNA encoding an apoptosis repressor with a CARD (ARC) which is expressed in both skeletal and cardiac muscle has been identified and characterized. ARC functions as an inhibitor of apoptosis and interacts selectively with caspases (Koseki, T. et al. (1998) Proc. Natl. Acad. Sci. USA 95:5156-5160). All of these interactions have clear effects on the control of apoptosis (reviewed in Chan S. L. and M. P. Mattson (1999) J. Neurosci. Res. 58:167-190; Salveson, G. S. and V. M. Dixit (1999) Proc. Natl. Acad. Sci. USA 96:10964-10967).

[0092] ES18 was identified as a potential regulator of apoptosis in mouse T-cells (Park, E. J. et al. (1999) Nuc. Acid. Res. 27:1524-1530). ES18 is 428 amino acids in length, contains an N-terminal proline-rich region, an acidic glutamic acid-rich domain, and a putative LXXLL nuclear receptor binding motif. The protein is preferentially expressed in lymph nodes and thymus. The level of ES18 expression increases in T-cell thymoma S49.1 in response to treatment with dexamethasone, staurosporine, or C2-ceramide, which induce apoptosis. ES18 may play a role in stimulating apoptotic cell death in T-cells.

[0093] The rat ventral prostate (RVP) is a model system for the study of hormone-regulated apoptosis. RVP epithelial cells undergo apoptosis in response to androgen deprivation. Messenger RNA (mRNA) transcripts that are up-regulated in the apoptotic RVP have been identified (Briehl, M. M. and Miesfeld, R. L. (1991) Mol. Endocrinol. 5:1381-1388). One such transcript encodes RVP.1, the precise role of which in apoptosis has not been determined. The human homolog of RVP.1, hRVP1, is 89% identical to the rat protein (Katahira, J. et al. (1997) J. Biol. Chem. 272:26652-26658). hRVP1 is 220 amino acids in length and contains four transmembrane domains. hRVP1 is highly expressed in the lung, intestine, and liver. Interestingly, hRVP1 functions as a low affinity receptor for the Clostridium perfringens enterotoxin, a causative agent of diarrhea in humans and other animals.

[0094] Cytokine-mediated apoptosis plays an important role in hematopoiesis and the immune response. Myeloid cells, which are the stem cell progenitors of macrophages, neutrophils, erythrocytes, and other blood cells, proliferate in response to specific cytokines such as granulocyte/macrophage-colony stimulating factor (GM-CSF) and interleukin-3 (IL-3). When deprived of GM-CSF or IL-3, myeloid cells undergo apoptosis. The murine requiem (req) gene encodes a putative transcription factor required for this apoptotic response in the myeloid cell line FDCP-1 (Gabig, T. G. et al. (1994) J. Biol. Chem. 269:29515-29519). The Req protein is 371 amino acids in length and contains a nuclear localization signal, a single Kruppel-type zinc finger, an acidic domain, and a cluster of four unique zinc-finger motifs enriched in cysteine and histidine residues involved in metal binding. Expression of req is not myeloid- or apoptosis-specific, suggesting that additional factors regulate Req activity in myeloid cell apoptosis.

[0095] Dysregulation of apoptosis has recently been recognized as a significant factor in the pathogenesis of many human diseases. For example, excessive cell survival caused by decreased apoptosis can contribute to disorders related to cell proliferation and the immune response. Such disorders include cancer, autoimmune diseases, viral infections, and inflammation. In contrast, excessive cell death caused by increased apoptosis can lead to degenerative and immunodeficiency disorders such as AIDS, neurodegenerative diseases, and myelodysplastic syndromes. (Thompson, C. B. (1995) Science 267:1456-1462.)

[0096] Dysregulation of apoptosis has recently been recognized as a significant factor in the pathogenesis of many human diseases. For example, excessive cell survival caused by decreased apoptosis can contribute to disorders related to cell proliferation and the immune response. Such disorders include cancer, autoimmune diseases, viral infections, and inflammation. In contrast, excessive cell death caused by increased apoptosis can lead to degenerative and immunodeficiency disorders such as AIDS, neurodegenerative diseases, and myelodysplastic syndromes. (Thompson, C. B. (1995) Science 267:1456-1462.)

[0097] Impaired regulation of apoptosis is also associated with loss of neurons in Alzheimer's disease. Alzheimer's disease is a progressive neurodegenerative disorder that is characterized by the formation of senile plaques and neurofibrillary tangles containing amyloid beta peptide. These plaques are found in limbic and association cortices of the brain, including hippocampus, temporal cortices, cingulate cortex, amygdala, nucleus basalis and locus caeruleus. B-amyloid peptide participates in signaling pathways that induce apoptosis and lead to the death of neurons (Kajkowski, C. et al. (2001) J. Biol. Chem. 276:18748-18756). Early in Alzheimer's pathology, physiological changes are visible in the cingulate cortex (Minoshima, S. et al. (1997) Annals of Neurology 42:85-94). In subjects with advanced Alzheimer's disease, accumulating plaques damage the neuronal architecture in limbic areas and eventually cripple the memory process.

[0098] Cancer

[0099] Cancer remains a major public health concern, and current preventative measures and treatments do not match the needs of most patients. Cancers, also called neoplasias, are characterized by continuous and uncontrolled cell proliferation. They can be divided into three categories: carcinomas, sarcomas, and leukemias. Carcinomas are malignant growths of soft epithelial cells that may infiltrate surrounding tissues and give rise to metastatic tumors. Sarcomas may be of epithelial origin or arise from connective tissue. Leukemias are progressive malignancies of blood-forming tissue characterized by proliferation of leukocytes and their precursors, and may be classified as myelogenous (granulocyte- or monocyte-derived) or lymphocytic (lymphocyte-derived). Tumorigenesis refers to the progression of a tumor's growth from its inception. Malignant cells may be quite similar to normal cells within the tissue of origin or may be undifferentiated (anaplastic). Tumor cells may possess few nuclei or one large polymorphic nucleus. Anaplastic cells may grow in a disorganized mass that is poorly vascularized and as a result contain large areas of ischemic necrosis. Differentiated neoplastic cells may secrete the same proteins as the tissue of origin. Cancers grow, infiltrate, invade, and destroy the surrounding tissue through direct seeding of body cavities or surfaces, through lymphatic spread, or through hematogenous spread. Cancer remains a major public health concern and current preventative measures and treatments do not match the needs of most patients. Understanding of the neoplastic process of tumorigenesis can be aided by the identification of molecular markers of prognostic and diagnostic importance.

[0100] Understanding of the neoplastic process can be aided by the identification of molecular markers of prognostic and diagnostic importance. Cancers are associated with oncoproteins which are capable of transforming normal cells into malignant cells. Some oncoproteins are mutant isoforms of the normal protein while others are abnormally expressed with respect to location or level of expression. Normal cell proliferation begins with binding of a growth factor to its receptor on the cell membrane, resulting in activation of a signal system that induces and activates nuclear regulatory factors to initiate DNA transcription, subsequently leading to cell division. Classes of oncoproteins known to affect the cell cycle controls include growth factors, growth factor receptors, intracellular signal transducers, nuclear transcription factors, and cell-cycle control proteins. Several types of cancer-specific genetic markers, such as tumor antigens and tumor suppressors, have also been identified.

[0101] Cancers or malignant tumors, which are characterized by continuous cell proliferation and cell death, can be classified into three categories: carcinomas, sarcomas, and leukemia. Reports show that approximately one in eight women contracts breast cancer and that approximately one in ten men over 50 years of age contracts prostate cancer. (Helzlsouer, K. J. (1994) Curr. Opin. Oncol. 6: 541-548; Harris, J. R. et al. (1992) N. Engl. J. Med. 327:319-328.)

[0102] Cancers are associated with the activation of oncogenes which are derived from normal cellular genes. These oncogenes encode oncoproteins which are capable of converting normal cells into malignant cells. Some oncoproteins are mutated isoforms of the normal protein, while other oncoproteins are abnormally expressed with respect to location or level of expression. The latter category of oncoproteins causes cancer by altering transcriptional control of cell proliferation. Five classes of oncoproteins are known to affect the cell cycle controls. These classes include growth factors, growth factor receptors, intracellular signal transducers, nuclear transcription factors, and cell-cycle control proteins. In some cases, oncogenes can be activated by retroviruses and DNA viruses. Oncogene activation occurs as a consequence of the integration of a viral genome into the DNA of the host cell. In these cases, more than one oncogene, capable of maintaining the infected cell in a condition of continuous cell division, may be activated.

[0103] Cancers are characterized by continuous or uncontrolled cell proliferation. Some cancers are associated with suppression of normal apoptotic cell death. Understanding of the neoplastic process can be aided by the identification of molecular markers of prognostic and diagnostic importance. Cancers are associated with oncoproteins which are capable of transforming normal cells into malignant cells. Some oncoproteins are mutant isoforms of the normal protein while others are abnormally expressed with respect to location or level of expression. Normal cell proliferation begins with binding of a growth factor to its receptor on the cell membrane, resulting in activation of a signal system that induces and activates nuclear regulatory factors to initiate DNA transcription, subsequently leading to cell division. Classes of oncoproteins known to affect the cell cycle controls include growth factors, growth factor receptors, intracellular signal transducers, nuclear transcription factors, and cell-cycle control proteins. Several types of cancer-specific genetic markers, such as tumor antigens and tumor suppressors, have also been identified.

[0104] Current forms of cancer treatment include the use of immunosuppressive drugs (Morisaki, T., Matsunaga H., et al. (2000) Anticancer Res. 20: 3363-3373; Geoerger, B., Kerr, K., et al. (2001) Cancer Res. 61: 1527-1532). The identification of proteins involved in cell signaling, and specifically proteins that act as receptors for immunosuppressant drugs, may facilitate the development of anti-tumor agents. For example, immunophilins are a family of conserved proteins found in both prokaryotes and eukaryotes that bind to immunosuppressive drugs with varying degrees of specificity. One such group of immunophilic proteins is the peptidyl-prolyl cis-trans isomerase (EC 5.2.1.8) family (PPIase, rotamase). These enzymes, first isolated from porcine kidney cortex, accelerate protein folding by catalyzing the cis-trans isomerization of proline imidic peptide bonds in oligopeptides (Fischer, G. and Schmid, F. X. (1990) Biochemistry 29: 2205-2212). Included within the immunophilin family are the cyclophilins (e.g., peptidyl-prolyl isomerase A or PPIA) and FK-binding protein (e.g., FKBP) subfamilies. Cyclophilins are multifunctional receptor proteins which participate in signal transduction activities, including those mediated by cyclosporin (or cyclosporine). The PPIase domain of each family is highly conserved between species. Although structurally distinct, these multifunctional receptor proteins are involved in numerous signal transduction pathways, and have been implicated in folding and trafficking events.

[0105] The immunophilin protein cyclophilin binds to the immunosuppressant drug cyclosporin A. FKBP, another immunophilin, binds to FK506 (or rapamycin). Rapamycin is an immunosuppressant agent that arrests cells in the G₁ phase of growth, inducing apoptosis. Like cyclophilin, this macrolide antibiotic (produced by Streptomyces tsukubaensis) acts by binding to ubiquitous, predominantly cytosolic immunophilin receptors. These immunophilin/immunosuppressant complexes (e.g., cyclophilin A/cyclosporin A (CypA/CsA) and FKBP12/FK506) achieve their therapeutic results through inhibition of the phosphatase calcineurin, a calcium/calmodulin-dependent protein kinase that participates in T-cell activation (Hamilton, G. S. and Steiner, J. P. (1998) J. Med. Chem. 41: 5119-5143). The murine fkbp51 gene is abundantly expressed in immunological tissues, including the thymus and T lymphocytes (Baughman, G., Wiederrecht, G. J., et al. (1995) Molec. Cell. Biol. 15: 4395-4402). FKBP12/rapamycin-directed immunosuppression occurs through binding to TOR (yeast) or FRAP (FKBP12-rapamycin-associated protein, in mammalian cells), the kinase target of rapamycin essential for maintaining normal cellular growth patterns. Dysfunctional TOR signaling has been linked to various human disorders including cancer (Metcalfe, S. M., Canman, C. E., et al. (1997) Oncogene 15: 1635-1642; Emami, S., Le Flock, N., et al. (2001) FASEB J. 15: 351-361), and autoimmunity (Damoiseaux, J. G., Beijleveld, L. J., et al. (1996) Transplantation 62: 994-1001).

[0106] Several cyclophilin isozymes have been identified, including cyclophilin B, cyclophilin C, mitochondrial matrix cyclophilin, bacterial cytosolic and periplasmic PPIases, and natural-killer cell cyclophilin-related protein possessing a cyclophilin-type PPIase domain, a putative tumor-recognition complex involved in the function of natural killer (NK) cells. These cells participate in the innate cellular immune response by lysing virally-infected cells or transformed cells. NK cells specifically target cells that have lost their expression of major histocompatibility complex (MHC) class I genes (common during tumorigenesis), endowing them with the potential for attenuating tumor growth. A 150-kDa molecule has been identified on the surface of human NK cells that possesses a domain which is highly homologous to cyclophilin/peptidyl-prolyl cis-trans isomerase. This cyclophilin-type protein may be a component of a putative tumor-recognition complex, a NK tumor recognition sequence (NK-TR) (Anderson, S. K., Gallinger, S., et al. (1993) Proc. Natl. Acad. Sci. USA 90: 542-546). The NKTR tumor recognition sequence mediates recognition between tumor cells and large granular lymphocytes (LGLs), a subpopulation of white blood cells (comprised of activated cytotoxic T cells and natural killer cells) capable of destroying tumor targets. The protein product of the NKTR gene presents on the surface of LGLs and facilitates binding to tumor targets. More recently, a mouse Nktr gene and promoter region have been located on chromosome 9. The gene encodes a NK-cell-specific 150-kDa protein (NK-TR) that is homologous to cyclophilin and other tumor-responsive proteins (Simons-Evelyn, M., Young, H. A. and Anderson, S. K. (1997) Genomics 40: 94-100).

[0107] Other proteins that interact with tumorigenic tissue include cytokines such as tumor necrosis factor (TNF). The TNF family of cytokines are produced by lymphocytes and macrophages, and can cause the lysis of transformed (tumor) endothelial cells. Endothelial protein 1 (Edp1) has been identified as a human gene activated transcriptionally by TNF-alpha in endothelial cells, and a TNF-alpha inducible Edp1 gene has been identified in the mouse (Swift, S., Blackburn, C., et al. (1998) Biochim. Biophys. Acta 1442: 394-398).

[0108] Oncogenes

[0109] Many oncogenes have been identified and characterized. These include growth factors such as sis, receptors such as erbA, erbB, neu, and ros, intracellular receptors such as src, yes, fps, abl, and met, protein-serine/threonine kinases such as mos and raf, nuclear transcription factors such as jun, fos, myc, N-myc, myb, ski, and rel, cell cycle control proteins such as RB and p53, mutated tumor-suppressor genes such as mdm2, Cip1, p16, and cyclin D, ras, set, can, sec, and gag R10. In particular, FOS encoded by fos, is a leucine-zipper-containing phosphoprotein located in the nucleus of cells. FOS forms a non-covalent complex with several other proteins to activate the transcription of growth-promoting proteins. (Bohmann, D. et al. (1987) Science 238:1386-1392; Cohen, D. R. and Curran, T. (1988) Mol. Cell. Biol. 8: 2063-2069; and van Straaten, F. et al. (1983) Proc. Natl. Acad. Sci. 80: 3188-3187.) can is a putative human oncogene associated with myeloid leukemogenesis and is activated as an oncogene by fusion of its 3′ half with other genes such as set. (von Lindern, M. et al. (1992) Mol. Cell. Biol. 12: 3346-3355.) SET, encoded by set, is shown to be a potent inhibitor of phosphatase 2A, a serine/threonine phosphatase that regulates diverse cellular processes. (Li, M. et al. (1996) J. Biol. Chem. 271: 11059-11062.) The Xenopus homolog of SET, NAP1, is found to interact specifically with B-type cyclins and plays an essential role in cell cycle regulation. (Kellogg, D. R. et al. (1995) J. Cell Biol. 130: 661-673.) SEC is the gene product of sec and is an oncoprotein active in tumors of secretory epithelium. (Lane, M. A. et al. (1990) Nuc. Acids Res. 18: 3068.) gag R10 is a leucine zipper-containing cytoplasmic protein of 23 kDa identified from chicken embryonic neuroretina cells and is encoded by a chimeric mRNA, RAV-1, which is capable of inducing cells to continuous cell proliferation. (Proux, V. et al. (1996) J. Biol. Chem. 271: 30790-30797.) S-100 are a family of small dimeric acidic calcium and zinc-binding proteins expressed abundantly in brain. These proteins play important roles in cell growth and differentiation, cell cycle regulation, and metabolic control. (Moncrief, N. D. et al. (1990) J. Mol. Evol. 30: 522-562; and Wicki, R. et al. (1996) Biochem. Biophys. Res. Commun. 227: 594-599.) rad1 is a yeast protein involved in DNA repair and recombination. (Sunnerhagen, P. et al. (1990) Mol. Cell. Biol. 10: 3750-3760.) Alpha-L-fucosidase is a lysosomal enzyme which hydrolyzes alpha-1,6 bond between fucose and the N-acetylglucosamine of the carbohydrate moieties of glycoproteins. Deficiency of alpha-L-fucosidase results in fucosidosis, a lysosomal storage disease. (Herissat, B. (1991) Biochem. J. 280: 309-316.)

[0110] Oncoproteins are encoded by genes, called oncogenes, that are derived from genes that normally control cell growth and development. Many oncogenes have been identified and characterized. These include growth factors such as sis, receptors such as erbA, erbB, neu, and ros, intracellular receptors such as src, yes, fps, abl, and met, protein-serine/threonine kinases such as mos and raf, nuclear transcription factors such as jun, fos, myc, N-myc, myb, ski, and rel, cell cycle control proteins such as RB and p53, mutated tumor-suppressor genes such as mdm12, Cip1, p16, and cyclin D, ras, set, can, sec, and gag R10.

[0111] Viral oncogenes are integrated into the human genome after infection of human cells by certain viruses. Examples of viral oncogenes include v-src, v-abl, and v-fps. Transformation of normal genes to oncogenes may also occur by chromosomal translocation. The Philadelphia chromosome, characteristic of chronic myeloid leukemia and a subset of acute lymphoblastic leukemias, results from a reciprocal translocation between chromosomes 9 and 22 that moves a truncated portion of the proto-oncogene c-abl to the breakpoint cluster region (bcr) on chromosome 22. The hybrid c-abl-bcr gene encodes a chimeric protein that has tyrosine kinase activity. In chronic myeloid leukemia, the chimeric protein has a molecular weight of 210 kd, whereas in acute leukemias a more active 180 kd tyrosine kinase is formed (Robbins, S. L. et al. (1994) Pathologic Basis of Disease, W. B. Saunders Co., Philadelphia Pa.).

[0112] The Wnt gene family of secreted signaling molecules is highly conserved throughout eukaryotic cells. Members of the Wnt family are involved in regulating chondrocyte differentiation within the cartilage template. Wnt-5a, Wnt-5b and Wnt-4 genes are expressed in chondrogenic regions of the chicken limb, Wnt-5a being expressed in the perichondrium (mesenchymal cells immediately surrounding the early cartilage template). Wnt-5a misexpression delays the maturation of chondrocytes and the onset of bone collar formation in chicken limb (Hartmann, C. and Tabin, C. J. (2000) Development 127:3141-3159).

[0113] RRP22protein/RAS-Related Proteins

[0114] Signal transduction is the general process by which cells respond to extracellular signals. In typical signal transduction pathways, binding of a signaling molecule such as a hormone, neurotransmitter, or growth factor to a cell membrane receptor is coupled to the action of an intracellular second messenger. G protein-coupled receptors (GPCRs) control intracellular processes through the activation of guanine nucleotide-binding proteins (G proteins). G proteins are heterotrimeric and consist of α, β, and γ subunits. The α subunits contain a guanine nucleotide binding domain and have GTPase activity. When GTP binds to α subunits, it dissociates from the β and γ subunits and interacts with cellular target molecules. Hydrolysis of GTP to GDP serves as a molecular switch controlling the interactions of the subunit with other proteins. The GDP bound form of the α subunit dissociates from its cellular target and reassociates with the β and γ subunits. A number of accessory proteins modulate G protein function by controlling their nucleotide phosphorylation state or membrane association. These regulatory molecules include exchange factors (GEFs) which stimulate GDP-GTP exchange, GTPase activating proteins (GAPs) which promote GTP hydrolysis, and guanine nucleotide dissociation inhibitors (GDIs) which inhibit guanine nucleotide dissociation and stabilize the GDP-bound form. G proteins can be classified into at least five subfamilies: Ras, Rho, Ran, Rab, and ADP-ribosylation factor, and they regulate various cell functions including cell growth and differentiation, cytoskeletal organization, and intracellular vesicle transport and secretion.

[0115] The Ras superfamily of small GTPases is involved in the regulation of a wide range of cellular signaling pathways. Ras family proteins are membrane-associated proteins acting as molecular switches that bind GTP and GDP, hydrolyzing GTP to GDP. In the active GTP-bound state Ras family proteins interact with a variety of cellular targets to activate downstream signaling pathways. For example, members of the Ras subfamily are essential in transducing signals from receptor tyrosine kinases (RTKs) to a series of serine/threonine kinases which control cell growth and differentiation. Activated Ras genes were initially found in human cancers and subsequent studies confirmed that Ras function is critical in the determination of whether cells continue to grow or become terminally differentiated (Barbacid, M. (1987) Annu. Rev. Biochem. 56:779-827, Treisman, R. (1994) Curr. Opin. Genet. Dev. 4:96-98). Mutant Ras proteins, which bind but can not hydrolyze GTP, are permanently activated, and cause continuous cell proliferation or cancer.

[0116] The Ras subfamily transduces signals from tyrosine kinase receptors, non-tyrosine kinase receptors, and heterotrimeric GPCRs (Fantl, W. J. et al. (1993) Annu. Rev. Biochem. 62:453-481; Woodrow, M. A. et al. (1993) J. Immunol. 150:3853-3861; and van Corven, E. J. et al. (1993) Proc. Natl. Acad. Sci. 90:1257-1261). Stimulation of cell surface receptors activates Ras which, in turn, activates cytoplasmic kinases that control cell growth and differentiation. The first Ras targets identified were the Raf kinases (Avruch, J. et al. (1994) Trends Biochem. Sci. 19:279-283). Interaction of Ras and Raf leads to activation of the MAP kinase cascade of serine/threonine kinases, which activate key transcription factors that control gene expression and protein synthesis (Barbacid, M. (1987) Ann. Rev. Biochem. 56:779-827; Treisman, R. (1994) Curr. Opin. Genet. Dev. 4:96-101). Mutated Ras proteins, which bind but do not hydrolyze GTP, are constitutively activated, and cause continuous cell proliferation and cancer (Bos, J. L. (1989) Cancer Res. 49:4682-4689; Grunicke, H. H. and Maly, K. (1993) Crit. Rev. Oncog. 4:389-402).

[0117] Many oncogenes have been identified and characterized. These include growth factors such as sis, receptors such as erbA, erbB, neu, and ros, intracellular receptors such as src, yes, fps, abl, and met, protein-serine/threonine kinases such as mos and raf, nuclear transcription factors such as jun, fos, myc, N-myc, myb, ski, and rel, cell cycle control proteins such as RB and p53, mutated tumor-suppressor genes such as mdm2, Cip1, p16, and cyclin D, ras, set, can, sec, and gag R10. In particular, FOS encoded by fos, is a leucine-zipper-containing phosphoprotein located in the nucleus of cells. FOS forms a non-covalent complex with several other proteins to activate the transcription of growth-promoting proteins. (Bohmann, D. et al. (1987>Science 238:1386-1392; Cohen, D. R. and Curran, T. (1988) Mol. Cell. Biol. 8: 2063-2069; and van Straaten, F. et al. (1983) Proc. Natl. Acad. Sci. 80: 3188-3187.) can is a putative human oncogene associated with myeloid leukemogenesis and is activated as an oncogene by fusion of its 3′ half with other genes such as set. (von Lindern, M. et al. (1992) Mol. Cell. Biol. 12: 3346-3355.) SET, encoded by set, is shown to be a potent inhibitor of phosphatase 2A, a serine/threonine phosphatase that regulates diverse cellular processes. (Li, M. et al. (1996) J. Biol. Chem. 271: 11059-11062.) The Xenopus homolog of SET, NAP1, is found to interact specifically with B-type cyclins and plays an essential role in cell cycle regulation. (Kellogg, D. R. et al. (1995) J. Cell Biol. 130: 661-673.) SEC is the gene product of sec and is an oncoprotein active in tumors of secretory epithelium. (Lane, M. A. et al. (1990) Nuc. Acids Res. 18: 3068.) gag R10 is a leucine zipper-containing cytoplasmic protein of 23 kDa identified from chicken embryonic neuroretina cells and is encoded by a chimeric mRNA, RAV-1, which is capable of inducing cells to continuous cell proliferation. (Proux, V. et al. (1996) J. Biol. Chem. 271: 30790-30797.) S-100 are a family of small dimeric acidic calcium and zinc-binding proteins expressed abundantly in brain. These proteins play important roles in cell growth and differentiation, cell cycle regulation, and metabolic control. (Moncrief, N. D. et al. (1990) J. Mol. Evol. 30: 522-562; and Wicki, R. et al. (1996) Biochem. Biophys. Res. Commun. 227: 594-599.) rad1 is a yeast protein involved in DNA repair and recombination. (Sunnerhagen, P. et al. (1990) Mol. Cell. Biol. 10: 3750-3760.) Alpha-L-fucosidase is a lysosomal enzyme which hydrolyzes alpha-1,6 bond between fucose and the N-acetylglucosamine of the carbohydrate moieties of glycoproteins. Deficiency of alpha-L-fucosidase results in fucosidosis, a lysosomal storage disease. (Herissat, B. (1991) Biochem. J. 280: 309-316.)

[0118] Ras regulates other signaling pathways by direct interaction with different cellular targets (Katz, M. E. and McCormick, F. (1997) Curr. Opin. Genet. Dev. 7:75-79). One such target is RalGDS, a guanine nucleotide dissociation stimulator for the Ras-like GTPase, Ral (Albright, C. F. et al. (1993) EMBO J. 12:339-347). RalGDS couples the Ras and Ral signaling pathways. Epidermal growth factor (EGF) stimulates the association of RalGDS with Ras in mammalian cells, which activates the GEF activity of RalGDS (Kikuchi, A. and Williams, L. T. (1996) J. Biol. Chem. 271:588-594; Urano, T. et al. (1996) EMBO J. 15:810-816). Ral activation by Ral-GDS leads to activation of Src, a tyrosine kinase that phosphorylates other molecules including transcription factors and components of the actin cytoskeleton (Goi, T. et al. (2000) EMBO J. 19:623-630). Ral interacts with a number of signaling molecules including Ral-binding protein, a GAP for the Rho-like GTPases; Cdc42 and Rac, which regulate cytoskeletal rearrangement; and phospholipase D1, which is involved in vesicular trafficking (Feig, L. A. et al. (1996) Trends Biochem. Sci. 21:438-441; Voss, M. et al. (1999) J. Biol. Chem. 274:34691-34698).

[0119] Nore1 was identified from a yeast two-hybrid screen as a protein that interacts with Ras and Ras-related protein, Rap1b (Vavvas, D. et al. (1998) J. Biol. Chem. 273:5439-5442). It is a basic protein (pI=9.4) of 413 amino acids that contains a cysteine-histidine-rich region predicted to be a diacylglycerol/phorbol ester binding site, a proline-rich region at its N-terminus that may be an SH3 binding domain, and a Ras/Rap binding domain located at its C-terminus. Nore1 binds Ras in vitro in a GTP-dependent manner. Experiments in vivo show that the association of Nore1 with Ras is dependent on EGF and 12-O-tetradecanoylphorbol-13-acetate activation in COS-7 cells and on EGF in KB cells.

[0120] Ras and other G proteins play roles in regulating the immune inflammatory response. Granulocytes, which include basophils, eosinophils, and neutrophils, play critical roles in inflammation. Eosinophils release toxic granule proteins, which kill microorganisms, and secrete prostaglandins, leukotrienes and cytokines, which amplify the inflammatory response. They sustain inflammation in allergic reactions and their malfunction can cause asthma and other allergic diseases. Interleukin-5 is a cytokine that regulates the growth, activation, and survival of eosinophils. The signal transduction mechanism of IL-5 in eosinophils involves the Ras-MAP kinase and Jak-Stat pathways (Pazdrak, K. et al. (1995) J. Exp. Med. 181:1827-1834; Adachi, T. and Ala, R. (1998) Am. J. Physiol. 275:C623-633). Raf-1 kinase activation by Ras is implicated in eosinophil degranulation.

[0121] Neutrophils migrate to inflammatory sites where they eliminate pathogens by phagocytosis and release toxic products from their granules that kill microorganisms. G proteins, including Ras, Ral, Rac1, and Rap1 regulate neutrophil function (M'Rabet, L. et al. (1999) J. Biol. Chem. 274:21847-21852). Rac1 may be involved in the respiratory burst of neutrophils. Ras and Rap1 are activated in response to the chemotactic agent, formyl methionine leucine phenylalanine (fMLP); the lipid mediator, platelet activating factor (PAF); and the cytokine, granulocyte-macrophage colony-stimulating factor (GM-CSF). Both Ras and Rap1 appear to play roles in neutrophil activation. Ral is activated by fMLP and PAF but not by GM-CSF and may be involved in chemotaxis, phagocytosis, or degranulation. Impairment of neutrophil function is associated with various inflammatory and autoimmune diseases.

[0122] RRP22 defines a new subgroup whose expression is limited to the central nervous system. The genes are located in the CpG-rich q12 region of chromosome 22 within a 40-kb region bounded by the EWS and BAM22 genes (Zucman-Rossi, J. et al. (1996) Genomics 38:247-254).

[0123] Activation of Ras family proteins is catalyzed by guanine nucleotide exchange factors (GEFs) which catalyze the dissociation of bound GDP and subsequent binding of GTP. A recently discovered RalGEF-like protein, RGL3, interacts with both Ras and the related protein Rit. Constitutively active Rit, like Ras, can induce oncogenic transformation, although since Rit fails to interact with most known Ras effector proteins, novel cellular targets may be involved in Rit transforming activity. RGL3 interacts with both Ras and Rit, and thus may act as a downstream effector for these proteins (Shao, H. and Andres, D. A. (2000) J. Biol. Chem. 275:26914-26924).

[0124] Tumor Antigens

[0125] Tumor antigens are cell surface molecules that are differentially expressed in tumor cells relative to non-tumor tissues. Tumor antigens make tumor cells immunologically distinct from normal cells and are potential diagnostics for human cancers. Several monoclonal antibodies have been identified which react specifically with cancerous cells such as T-cell acute lymphoblastic leukemia and neuroblastoma (Minegishi et al. (1989) Leukemia Res. 13:43-51; Takagi et al. (1995) Int. J. Cancer 61:706-715). In addition, the discovery of high level expression of the HER2 gene in breast tumors has led to the development of therapeutic treatments (Liu et al. (1992) Oncogene 7: 1027-1032; Kern (1993) Am. J. Respir. Cell Mol. Biol. 9:448-454). Tumor antigens are found on the cell surface and have been characterized either as membrane proteins or glycoproteins. For example, MAGE genes encode a family of tumor antigens recognized on melanoma cell surfaces by autologous cytolytic T lymphocytes. Among the 12 human MAGE genes isolated, half are differentially expressed in tumors of various histological types (De Plaen et al. (1994) Immunogenetics 40:360-369). None of the 12 MAGE genes, however, is expressed in healthy tissues except testis and placenta.

[0126] Breast Cancer

[0127] There are more than 180,000 new cases of breast cancer diagnosed each year, and the mortality rate for breast cancer approaches 10% of all deaths in females between the ages of 45-54 (K. Gish (1999) AWIS Magazine 28:7-10). However the survival rate based on early diagnosis of localized breast cancer is extremely high (97%), compared with the advanced stage of the disease in which the tumor has spread beyond the breast (22%). Current procedures for clinical breast examination are lacking in sensitivity and specificity, and efforts are underway to develop comprehensive gene expression profiles for breast cancer that may be used in conjunction with conventional screening methods to improve diagnosis and prognosis of this disease (Perou, C. M. et al. (2000) Nature 406:747-752).

[0128] Mutations in two genes, BRCA1 and BRCA2, are known to greatly predispose a woman to breast cancer and may be passed on from parents to children (Gish, K. (1999) AWIS Magazine 28:7-10). However, this type of hereditary breast cancer accounts for only about 5% to 9% of breast cancers, while the vast majority of breast cancer is due to non-inherited mutations that occur in breast epithelial cells.

[0129] The relationship between expression of epidermal growth factor (EGF) and its receptor, EGFR, to human mammary carcinoma has been particularly well studied. (See Khazaie, K. et al. (1993) Cancer and Metastasis Rev. 12:255-274, and references cited therein for a review of this area.) Overexpression of EGFR, particularly coupled with down-regulation of the estrogen receptor, is a marker of poor prognosis in breast cancer patients. In addition, EGFR expression in breast tumor metastases is frequently elevated relative to the primary tumor, suggesting that EGFR is involved in tumor progression and metastasis. This is supported by accumulating evidence that EGF has effects on cell functions related to metastatic potential, such as cell motility, chemotaxis, secretion and differentiation. Changes in expression of other members of the erbB receptor family, of which EGFR is one, have also been implicated in breast cancer. The abundance of erbB receptors, such as HER-2/neu, HER-3, and HER-4, and their ligands in breast cancer points to their functional importance in the pathogenesis of the disease, and may therefore provide targets for therapy of the disease (Bacus, S. S. et al. (1994) Am. J. Clin. Pathol. 102:S13-S24). Other known markers of breast cancer include a human secreted frizzled protein mRNA that is downregulated in breast tumors; the matrix G1a protein which is overexpressed is human breast carcinoma cells; Drg1 or RTP, a gene whose expression is diminished in colon, breast, and prostate tumors; maspin, a tumor suppressor gene downregulated in invasive breast carcinomas; and CaN19, a member of the S100 protein family, all of which are down regulated in mammary carcinoma cells relative to normal mammary epithelial cells (Zhou, Z. et al. (1998) Int. J. Cancer 78:95-99; Chen, L. et al. (1990) Oncogene 5:1391-1395; Ulrix, W. et al (1999) FEBS Lett 455:23-26; Sager, R. et al. (1996) Curr. Top. Microbiol. Immunol. 213:51-64; and Lee, S. W. et al. (1992) Proc. Natl. Acad. Sci. USA 89:2504-2508).

[0130] Cell lines derived from human mammary epithelial cells at various stages of breast cancer provide a useful model to study the process of malignant transformation and tumor progression as it has been shown that these cell lines retain many of the properties of their parental tumors for lengthy culture periods (Wistuba, I. I. et al. (1998) Clin. Cancer Res. 4:2931-2938). Such a model is particularly useful for comparing phenotypic and molecular characteristics of human mammary epithelial cells at various stages of malignant transformation.

[0131] Tumor Suppressors

[0132] Tumor suppressor genes are generally defined as genetic elements whose loss or inactivation contributes to the deregulation of cell proliferation and the pathogenesis and progression of cancer. Tumor suppressor genes normally function to control or inhibit cell growth in response to stress and to limit the proliferative life span of the cell. Several tumor suppressor genes have been identified including the genes encoding the retinoblastoma (Rb) protein, p53, and the breast cancer 1 and 2 proteins (BRCA1 and BRCA2). Mutations in these genes are associated with acquired and inherited genetic predisposition to the development of certain cancers.

[0133] The role of p53 in the pathogenesis of cancer has been extensively studied. (Reviewed in Aggarwal, M. L. et al. (1998) J. Biol. Chem. 273:1-4; Levine, A. (1997) Cell 88:323-331.) About 50% of all human cancers contain mutations in the p53 gene. These mutations result in either the absence of functional p53 or, more commonly, a defective form of p53 which is overexpressed. p53 is a transcription factor that contains a central core domain required for DNA binding. Most cancer-associated mutations in p53 localize to this domain. In normal proliferating cells, p53 is expressed at low levels and is rapidly degraded. p53 expression and activity is induced in response to DNA damage, abortive mitosis, and other stressful stimuli. In these instances, p53 induces apoptosis or arrests cell growth until the stress is removed. Downstream effectors of p53 activity include apoptosis-specific proteins and cell cycle regulatory proteins, including Rb, oncogene products, cyclins, and cell cycle-dependent kinases.

[0134] The metastasis-suppressor gene KAI1 (CD82) has been reported to be related to the tumor suppressor gene p53. KAI1 is involved in the progression of human prostatic cancer and possibly lung and breast cancers when expression is decreased. KAI1 encodes a member of a structurally distinct family of leukocyte surface glycoproteins. The family is known as either the tetraspan transmembrane protein family or transmembrane 4 superfamily (TM4SF) as the members of this family span the plasma membrane four times. The family is composed of integral membrane proteins having a N-terminal membrane-anchoring domain which functions as both a membrane anchor and a translocation signal during protein biosynthesis. The N-terminal membrane-anchoring domain is not cleaved during biosynthesis. TM4SF proteins have three additional transmembrane regions, seven or more conserved cysteine residues, are similar in size (218 to 284 residues), and all have a large extracellular hydrophilic domain with three potential N-glycosylation sites. The promoter region contains many putative binding motifs for various transcription factors, including five AP2 sites and nine SpI sites. Gene structure comparisons of KAI1 and seven other members of the TM4SF indicate that the splicing sites relative to the different structural domains of the predicted proteins are conserved. This suggests that these genes are related evolutionarily and arose through gene duplication and divergent evolution (Levy, S. et al. (1991) J. Biol. Chem. 266:14597-14602; Dong, J. T. et al. (1995) Science 268:884-886; Dong, J. T. et al., (1997) Genomics 41:25-32).

[0135] The Leucine-rich gene-Glioma Inactivated (LGI1) protein shares homology with a number of transmembrane and extracellular proteins which function as receptors and adhesion proteins. LGI1 is encoded by an LLR (leucine-rich, repeat-containing) gene and maps to 10q24. LGI1 has four LLRs which are flanked by cysteine-rich regions and one transmembrane domain (Somerville, R. P., et al. (2000) Mamm. Genome 11:622-627). LGI1 expression is seen predominantly in neural tissues, especially brain. The loss of tumor suppressor activity is seen in the inactivation of the LGI1 protein which occurs during the transition from low to high-grade tumors in malignant gliomas. The reduction of LGI1 expression in low grade brain tumors and its significant reduction or absence of expression in malignant gliomas suggests that it could be used for diagnosis of glial tumor progression (Chernova, O. B., et al. (1998) Oncogene 17:2873-2881).

[0136] The ST13 tumor suppressor was identified in a screen for factors related to colorectal carcinomas by subtractive hybridization between cDNA of normal mucosal tissues and mRNA of colorectal carcinoma tissues (Cao, J. et al. (1997) J. Cancer Res. Clin. Oncol. 123:447-451). ST13 is down-regulated in human colorectal carcinomas.

[0137] Mutations in the von Hippel-Lindau (VHL) tumor suppressor gene are associated with retinal and central nervous system hemangioblastomas, clear cell renal carcinomas, and pheochromocytomas (Hoffman, M. et al. (2001) Hum. Mol. Genet. 10:1019-1027; Kamada, M. (2001) Cancer Res. 61:4184-4189). Tumor progression is linked to defects or inactivation of the VHL gene. VHL regulates the expression of transforming growth factor-α, the GLUT-1 glucose transporter and vascular endothelial growth factor. The VHL protein associates with elongin B, elongin C, Cu12 and Rbx1 to form a complex that regulates the transcriptional activator hypoxia-inducible factor (HIF). HIF induces genes involved in angiogenesis such as vascular endothelial growth factor and platelet-derived growth factor B. Loss of control of HIF caused by defects in VHL results in the excessive production of angiogenic peptides. VHL may play roles in inhibition of angiogenesis, cell cycle control, fibronectin matrix assembly, cell adhesion, and proteolysis.

[0138] Mutations in tumor suppressor genes are a common feature of many cancers and often appear to affect a critical step in the pathogenesis and progression of tumors. Accordingly, Chang, F. et al. (1995; J. Clin. Oncol. 13: 1009-1022) suggest that it may be possible to use either the gene or an antibody to the expressed protein 1) to screen patients at increased risk for cancer, 2) to aid in diagnosis made by traditional methods, and 3) to assess the prognosis of individual cancer patients. In addition, Hamada, K et al. (1996; Cancer Res. 56:3047-3054) are investigating the introduction of p53 into cervical cancer cells via an adenoviral vector as an experimental therapy for cervical cancer.

[0139] The PR-domain genes were recently recognized as playing a role in human tumorigenesis. PR-domain genes normally produce two protein products: the PR-plus product, which contains the PR domain, and the PR-minus product which lacks this domain. In cancer cells, PR-plus is disrupted or overexpressed, while PR-minus is present or overexpressed. The imbalance in the amount of these two proteins appears to be an important cause of malignancy (Jiang, G. L. and Huang, S. (2000) Histol. Histopathol. 15:109-117).

[0140] Many neoplastic disorders in humans can be attributed to inappropriate gene transcription. Malignant cell growth may result from either excessive expression of tumor promoting genes or insufficient expression of tumor suppressor genes (Cleary, M. L. (1992) Cancer Surv. 15:89-104). Chromosomal translocations may also produce chimeric loci which fuse the coding sequence of one gene with the regulatory regions of a second unrelated gene. An important class of transcriptional regulators are the zinc finger proteins. The zinc finger motif, which binds zinc ions, generally contains tandem repeats of about 30 amino acids consisting of periodically spaced cysteine and histidine residues. Examples of this sequence pattern include the C2H2-type, C4-type, and C3HC4-type zinc fingers, and the PHD domain (Lewin, supra; Aasland, R., et al. (1995) Trends Biochem. Sci. 20:56-59). One clinically relevant zinc-finger protein is WT1, a tumor-suppressor protein that is inactivated in children with Wilm's tumor. The oncogene bcl-6, which plays an important role in large-cell lymphoma, is also a zinc-finger protein (Papavassiliou, A. G. (1995) N. Engl. J. Med. 332:45-47).

[0141] Tumor Responsive Proteins

[0142] Cancers, also called neoplasias, are characterized by continuous and uncontrolled cell proliferation. They can be divided into three categories: carcinomas, sarcomas, and leukemias. Carcinomas are malignant growths of soft epithelial cells that may infiltrate surrounding tissues and give rise to metastatic tumors. Sarcomas may be of epithelial origin or arise from connective tissue. Leukemias are progressive malignancies of blood-forming tissue characterized by proliferation of leukocytes and their precursors, and may be classified as myelogenous (granulocyte- or monocyte-derived) or lymphocytic (lymphocyte-derived). Tumorigenesis refers to the progression of a tumor's growth from its inception. Malignant cells may be quite similar to normal cells within the tissue of origin or may be undifferentiated (anaplastic). Tumor cells may possess few nuclei or one large polymorphic nucleus. Anaplastic cells may grow in a disorganized mass that is poorly vascularized and as a result contains large areas of ischemic necrosis. Differentiated neoplastic cells may secrete the same proteins as the tissue of origin. Cancers grow, infiltrate, invade, and destroy the surrounding tissue through direct seeding of body cavities or surfaces, through lymphatic spread, or through hematogenous spread. Cancer remains a major public health concern and current preventative measures and treatments do not match the needs of most patients. Understanding of the neoplastic process of tumorigenesis can be aided by the identification of molecular markers of prognostic and diagnostic importance.

[0143] Current forms of cancer treatment include the use of immunosuppressive drugs (Morisaki, T. et al. (2000) Anticancer Res. 20: 3363-3373; Geoerger, B. et al. (2001) Cancer Res. 61: 1527-1532). The identification of proteins involved in cell signaling, and specifically proteins that act as receptors for immunosuppressant drugs, may facilitate the development of anti-tumor agents. For example, immunophilins are a family of conserved proteins found in both prokaryotes and eukaryotes that bind to immunosuppressive drugs with varying degrees of specificity. One such group of immunophilic proteins is the peptidyl-prolyl cis-trans isomerase (EC 5.2.1.8) family (PPIase, rotamase). These enzymes, first isolated from porcine kidney cortex, accelerate protein folding by catalyzing the cis-trans isomerization of proline imidic peptide bonds in oligopeptides (Fischer, G. and Schmid, F. X. (1990) Biochemistry 29: 2205-2212). Included within the immunophilin family are the cyclophilins (e.g., peptidyl-prolyl isomerase A or PPIA) and FK-binding protein (e.g., FKBP) subfamilies. Cyclophilins are multifunctional receptor proteins which participate in signal transduction activities, including those mediated by cyclosporin (or cyclosporine). The PPIase domain of each family is highly conserved between species. Although structurally distinct, these multifunctional receptor proteins are involved in numerous signal transduction pathways, and have been implicated in folding and trafficking events.

[0144] The immunophilin protein cyclophilin binds to the immunosuppressant drug cyclosporin A. FKBP, another immunophilin, binds to FK506 (or rapamycin). Rapamycin is an immunosuppressant agent that arrests cells in the G₁ phase of growth, inducing apoptosis. Like cyclophilin, this macrolide antibiotic (produced by Streptomyces tsukubaensis) acts by binding to ubiquitous, predominantly cytosolic immunophilin receptors. These immunophilin/immunosuppressant complexes (e.g., cyclophilin A/cyclosporin A (CypA/CsA) and FKBP12/FK506) achieve their therapeutic results through inhibition of the phosphatase calcineurin, a calcium/calmodulin-dependent protein kinase that participates in T-cell activation (Hamilton, G. S. and Steiner, J. P. (1998) J. Med. Chem. 41: 5119-5143). The murine fkbp51 gene is abundantly expressed in immunological tissues, including the thymus and T lymphocytes (Baughman, G. et al. (1995) Molec. Cell. Biol. 15: 4395-4402). FKBP12/rapamycin-directed immunosuppression occurs through binding to TOR (yeast) or FRAP (FKBP12-rapamycin-associated protein, in mammalian cells), the kinase target of rapamycin essential for maintaining normal cellular growth patterns. Dysfunctional TOR signaling has been linked to various human disorders including cancer (Metcalfe, S. M. et al. (1997) Oncogene 15: 1635-1642; Emami, S. et al. (2001) FASEB J. 15: 351-361), and autoimmunity (Damoiseaux, J. G. et al. (1996) Transplantation 62: 994-1001).

[0145] Several cyclophilin isozymes have been identified, including cyclophilin B, cyclophilin C, mitochondrial matrix cyclophilin, bacterial cytosolic and periplasmic PPIases, and natural-killer cell cyclophilin-related protein possessing a cyclophilin-type PPIase domain, a putative tumor-recognition complex involved in the function of natural killer (NK) cells. These cells participate in the innate cellular immune response by lysing virally-infected cells or transformed cells. NK cells specifically target cells that have lost their expression of major histocompatibility complex (MHC) class I genes (common during tumorigenesis), endowing them with the potential for attenuating tumor growth. A 150-kDa molecule has been identified on the surface of human NK cells that possesses a domain which is highly homologous to cyclophilin/peptidyl-prolyl cis-trans isomerase. This cyclophilin-type protein may be a component of a putative tumor-recognition complex, a NK tumor recognition sequence (NK-TR) (Anderson, S. K. et al. (1993) Proc. Natl. Acad. Sci. USA 90: 542-546). The NKTR tumor recognition sequence mediates recognition between tumor cells and large granular lymphocytes (LGLs), a subpopulation of white blood cells (comprised of activated cytotoxic T cells and natural killer cells) capable of destroying tumor targets. The protein product of the NKTR gene presents on the surface of LGLs and facilitates binding to tumor targets. More recently, a mouse Nktr gene and promoter region have been located on chromosome 9. The gene encodes a NK-cell-specific 150-kDa protein (NK-TR) that is homologous to cyclophilin and other tumor-responsive proteins (Simons-Evelyn, M. et al. (1997) Genomics 40: 94-100).

[0146] Other proteins that interact with tumorigenic tissue include cytokines such as tumor necrosis factor (TNF). The TNF family of cytokines are produced by lymphocytes and macrophages, and can cause the lysis of transformed (tumor) endothelial cells. Endothelial protein 1 (Edp1) has been identified as a human gene activated transcriptionally by TNF-alpha in endothelial cells, and a TNF-alpha inducible Edp1 gene has been identified in the mouse (Swift, S. et al. (1998) Biochim. Biophys. Acta 1442: 394-398).

[0147] Aging and Senescence

[0148] Studies of the aging process or senescence have shown a number of characteristic cellular and molecular changes (Fauci et al. (1998) Harrison's Principles of Internal Medicine, McGraw-Hill, New York N.Y., p.37). These characteristics include increases in chromosome structural abnormalities, DNA cross-linking, incidence of single-stranded breaks in DNA, losses in DNA methylation, and degradation of telomere regions. In addition to these DNA changes, post-translational alterations of proteins increase including, deamidation, oxidation, cross-linking, and nonenzymatic glycation. Still further molecular changes occur in the mitochondria of aging cells through deterioration of structure. These changes eventually contribute to decreased function in every organ of the body.

[0149] Lung Cancer

[0150] Lung cancer is the leading cause of cancer death for men and the second leading cause of cancer death for women in the U.S. Lung cancers are divided into four histopathologically distinct groups. Three groups (squamous cell carcinoma, adenocarcinoma, and large cell carcinoma) are classified as non-small cell lung cancers (NSCLCs). The fourth group of cancers is referred to as small cell lung cancer. (SCLC). Deletions on chromosome 3 are common in this disease and are thought to indicate the presence of a tumor suppressor gene in this region. Activating mutations in K-ras are commonly found in lung cancer and are the basis of one of the mouse models for the disease.

[0151] Steroid Hormones

[0152] Glucocorticoids are naturally occurring hormones that prevent or suppress inflammation and immune responses when administered at pharmacological doses. At the molecular level, unbound glucocorticoids readily cross cell membranes and bind with high affinity to specific cytoplasmic receptors. Subsequent to binding, transcription and, ultimately, protein synthesis are affected. The result can include inhibition of leukocyte infiltration at the site of inflammation, interference in the function of mediators of inflammatory response, and suppression of humoral immune responses. The antiinflammatory actions of corticosteroids are thought to involve phospholipase A2 inhibitory proteins, collectively called lipocortins. Lipocortins, in turn, control the biosynthesis of potent mediators of inflammation such as prostaglandins and leukotrienes by inhibiting the release of the precursor molecule arachidonic acid. Further, corticosteroids inhibit eosinophil, basophil, and airway epithelial cell function by regulation of cytokines that mediate the inflammatory response. They inhibit leukocyte infiltration at the site of inflammation, interfere in the function of mediators of the inflammatory response, and suppress the humoral immune response. Corticosteroids are used to treat allergies, asthma, arthritis, and skin conditions. Beclomethasone is a synthetic glucocorticoid that is used to treat steroid-dependent asthma, to relieve symptoms associated with allergic or nonallergic (vasomotor) rhinitis, or to prevent recurrent nasal polyps following surgical removal. The anti-inflammatory and vasoconstrictive effects of intranasal beclomethasone are 5000 times greater than those produced by hydrocortisone.

[0153] Expression Profiling

[0154] Array technology can provide a simple way to explore the expression of a single polymorphic gene or the expression profile of a large number of related or unrelated genes. When the expression of a single gene is examined, arrays are employed to detect the expression of a specific gene or its variants. When an expression profile is examined, arrays provide a platform for identifying genes that are tissue specific, are affected by a substance being tested in a toxicology assay, are part of a signaling cascade, carry out housekeeping functions, or are specifically related to a particular genetic predisposition, condition, disease, or disorder.

[0155] The discovery of new proteins associated with cell growth, differentiation, and death, and the polynucleotides encoding them, satisfies a need in the art by providing new compositions which are useful in the diagnosis, prevention, and treatment of cell proliferative disorders including cancer, developmental disorders, neurological disorders, autoimmune/inflammatory disorders, reproductive disorders, and disorders of the placenta, and in the assessment of the effects of exogenous compounds on the expression of nucleic acid and amino acid sequences of proteins associated with cell growth, differentiation, and death.

SUMMARY OF THE INVENTION

[0156] The invention features purified polypeptides, proteins associated with cell growth, differentiation, and death, referred to collectively as “CGDD” and individually as “CGDD-1,” “CGDD-2,” “CGDD-3,” “CGDD-4,” “CGDD-5,” “CGDD-6,” “CGDD-7,” “CGDD-8,” “CGDD-9,” “CGDD-10,” “CGDD-11,” “CGDD-12,” “CGDD-13,” “CGDD-14,” “CGDD-15,” “CGDD-16,” “CGDD-17,” “CGDD-18,” “CGDD-19,” “CGDD-20,” and “CGDD-21.” In one aspect, the invention provides an isolated polypeptide selected from the group consisting of a) a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO:1-21, b) a polypeptide comprising a naturally occurring amino acid sequence at least 90% identical to an amino acid sequence selected from the group consisting of SEQ ID NO:1-21, c) a biologically active fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO:1-21, and d) an immunogenic fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO:1-21. In one alternative, the invention provides an isolated polypeptide comprising the amino acid sequence of SEQ ID NO:1-21.

[0157] The invention further provides an isolated polynucleotide encoding a polypeptide selected from the group consisting of a) a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO:1-21, b) a polypeptide comprising a naturally occurring amino acid sequence at least 90% identical to an amino acid sequence selected from the group consisting of SEQ ID NO:1-21, c) a biologically active fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO:1-21, and d) an immunogenic fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO:1-21. In one alternative, the polynucleotide encodes a polypeptide selected from the group consisting of SEQ ID NO:1-21. In another alternative, the polynucleotide is selected from the group consisting of SEQ ID NO:22-42.

[0158] Additionally, the invention provides a recombinant polynucleotide comprising a promoter sequence operably linked to a polynucleotide encoding a polypeptide selected from the group consisting of a) a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO:1-21, b) a polypeptide comprising a naturally occurring amino acid sequence at least. 90% identical to an amino acid sequence selected from the group consisting of SEQ ID NO:1-21, c) a biologically active fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO:1-21, and d) an immunogenic fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO:1-21. In one alternative, the invention provides a cell transformed with the recombinant polynucleotide. In another alternative, the invention provides a transgenic organism comprising the recombinant polynucleotide.

[0159] The invention also provides a method for producing a polypeptide selected from the group consisting of a) a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO:1-21, b) a polypeptide comprising a naturally occurring amino acid sequence at least 90% identical to an amino acid sequence selected from the group consisting of SEQ ID NO:1-21, c) a biologically active fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO:1-21, and d) an immunogenic fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO:1-21. The method comprises a) culturing a cell under conditions suitable for expression of the polypeptide, wherein said cell is transformed with a recombinant polynucleotide comprising a promoter sequence operably linked to a polynucleotide encoding the polypeptide, and b) recovering the polypeptide so expressed.

[0160] Additionally, the invention provides an isolated antibody which specifically binds to a polypeptide selected from the group consisting of a) a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO:1-21, b) a polypeptide comprising a naturally occurring amino acid sequence at least 90% identical to an amino acid sequence selected from the group consisting of SEQ ID NO:1-21, c) a biologically active fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO:1-21, and d) an immunogenic fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO:1-21.

[0161] The invention further provides an isolated polynucleotide selected from the group consisting of a) a polynucleotide comprising a polynucleotide sequence selected from the group consisting of SEQ ID NO:22-42, b) a polynucleotide comprising a naturally occurring polynucleotide sequence at least 90% identical to a polynucleotide sequence selected from the group consisting of SEQ ID NO:22-42, c) a polynucleotide complementary to the polynucleotide of a), d) a polynucleotide complementary to the polynucleotide of b), and e) an RNA equivalent of a)-d). In one alternative, the polynucleotide comprises at least 60 contiguous nucleotides.

[0162] Additionally, the invention provides a method for detecting a target polynucleotide in a sample, said target polynucleotide having a sequence of a polynucleotide selected from the group consisting of a) a polynucleotide comprising a polynucleotide sequence selected from the group consisting of SEQ ID NO:22-42, b) a polynucleotide comprising a naturally occurring polynucleotide sequence at least 90% identical to a polynucleotide sequence selected from the group consisting of SEQ ID NO:22-42, c) a polynucleotide complementary to the polynucleotide of a), d) a polynucleotide complementary to the polynucleotide of b), and e) an RNA equivalent of a)-d). The method comprises a) hybridizing the sample with a probe comprising at least 20 contiguous nucleotides comprising a sequence complementary to said target polynucleotide in the sample, and which probe specifically hybridizes to said target polynucleotide, under conditions whereby a hybridization complex is formed between said probe and said target polynucleotide or fragments thereof, and b) detecting the presence or absence of said hybridization complex, and optionally, if present, the amount thereof. In one alternative, the probe comprises at least 60 contiguous nucleotides.

[0163] The invention further provides a method for detecting a target polynucleotide in a sample, said target polynucleotide having a sequence of a polynucleotide selected from the group consisting of a) a polynucleotide comprising a polynucleotide sequence selected from the group consisting of SEQ ID NO:22-42, b) a polynucleotide comprising a naturally occurring polynucleotide sequence at least 90% identical to a polynucleotide sequence selected from the group consisting of SEQ ID NO:22-42, c) a polynucleotide complementary to the polynucleotide of a), d) a polynucleotide complementary to the polynucleotide of b), and e) an RNA equivalent of a)-d). The method comprises a) amplifying said target polynucleotide or fragment thereof using polymerase chain reaction amplification, and b) detecting the presence or absence of said amplified target polynucleotide or fragment thereof, and, optionally, if present, the amount thereof.

[0164] The invention further provides a composition comprising an effective amount of a polypeptide selected from the group consisting of a) a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO:1-21, b) a polypeptide comprising a naturally occurring amino acid sequence at least 90% identical to an amino acid sequence selected from the group consisting of SEQ ID NO:1-21, c) a biologically active fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO:1-21, and d) an immunogenic fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO:1-21, and a pharmaceutically acceptable excipient. In one embodiment, the composition comprises an amino acid sequence selected from the group consisting of SEQ ID NO:1-21. The invention additionally provides a method of treating a disease or condition associated with decreased expression of functional CGDD, comprising administering to a patient in need of such treatment the composition.

[0165] The invention also provides a method for screening a compound for effectiveness as an agonist of a polypeptide selected from the group consisting of a) a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO:1-21, b) a polypeptide comprising a naturally occurring amino acid sequence at least 90% identical to an amino acid sequence selected from the group consisting of SEQ ID NO:1-21, c) a biologically active fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO:1-21, and d) an immunogenic fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO:1-21. The method comprises a) exposing a sample comprising the polypeptide to a compound, and b) detecting agonist activity in the sample. In one alternative, the invention provides a composition comprising an agonist compound identified by the method and a pharmaceutically acceptable excipient. In another alternative, the invention provides a method of treating a disease or condition associated with decreased expression of functional CGDD, comprising administering to a patient in need of such treatment the composition.

[0166] Additionally, the invention provides a method for screening a compound for effectiveness as an antagonist of a polypeptide selected from the group consisting of a) a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO:1-21, b) a polypeptide comprising a naturally occurring amino acid sequence at least 90% identical to an amino acid sequence selected from the group consisting of SEQ ID NO:1-21, c) a biologically active fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO:1-21, and d) an immunogenic fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO:1-21. The method comprises a) exposing a sample comprising the polypeptide to a compound, and b) detecting antagonist activity in the sample. In one alternative, the invention provides a composition comprising an antagonist compound identified by the method and a pharmaceutically acceptable excipient. In another alternative, the invention provides a method of treating a disease or condition associated with overexpression of functional CGDD, comprising administering to a patient in need of such treatment the composition.

[0167] The invention further provides a method of screening for a compound that specifically binds to a polypeptide selected from the group consisting of a) a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO:1-21 b) a polypeptide comprising a naturally occurring amino acid sequence at least 90% identical to an amino acid sequence selected from the group consisting of SEQ ID NO:1-21, c) a biologically active fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO:1-21, and d) an immunogenic fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO:1-21. The method comprises a) combining the polypeptide with at least one test compound under suitable conditions, and b) detecting binding of the polypeptide to the test compound, thereby identifying a compound that specifically binds to the polypeptide.

[0168] The invention further provides a method of screening for a compound that modulates the activity of a polypeptide selected from the group consisting of a) a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO:1-21, b) a polypeptide comprising a naturally occurring amino acid sequence at least 90% identical to an amino acid sequence selected from the group consisting of SEQ ID NO:1-21, c) a biologically active fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO:1-21, and d) an immunogenic fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO:1-21. The method comprises a) combining the polypeptide with at least one test compound under conditions permissive for the activity of the polypeptide, b) assessing the activity of the polypeptide in the presence of the test compound, and c) comparing the activity of the polypeptide in the presence of the test compound with the activity of the polypeptide in the absence of the test compound, wherein a change in the activity of the polypeptide in the presence of the test compound is indicative of a compound that modulates the activity of the polypeptide.

[0169] The invention further provides a method for screening a compound for effectiveness in altering expression of a target polynucleotide, wherein said target polynucleotide comprises a polynucleotide sequence selected from the group consisting of SEQ ID NO:22-42, the method comprising a) exposing a sample comprising the target polynucleotide to a compound, b) detecting altered expression of the target polynucleotide, and c) comparing the expression of the target polynucleotide in the presence of varying amounts of the compound and in the absence of the compound.

[0170] The invention further provides a method for assessing toxicity of a test compound, said method comprising a) treating a biological sample containing nucleic acids with the test compound; b) hybridizing the nucleic acids of the treated biological sample with a probe comprising at least 20 contiguous nucleotides of a polynucleotide selected from the group consisting of i) a polynucleotide comprising a polynucleotide sequence selected from the group consisting of SEQ ID NO:22-42, ii) a polynucleotide comprising a naturally occurring polynucleotide sequence at least 90% identical to a polynucleotide sequence selected from the group consisting of SEQ ID NO:22-42, iii) a polynucleotide having a sequence complementary to i), iv) a polynucleotide complementary to the polynucleotide of ii), and v) an RNA equivalent of i)-iv). Hybridization occurs under conditions whereby a specific hybridization complex is formed between said probe and a target polynucleotide in the biological sample, said target polynucleotide selected from the group consisting of i) a polynucleotide comprising a polynucleotide sequence selected from the group consisting of SEQ ID NO:22-42, ii) a polynucleotide comprising a naturally occurring polynucleotide sequence at least 90% identical to a polynucleotide sequence selected from the group consisting of SEQ ID NO:22-42, iii) a polynucleotide complementary to the polynucleotide of i), iv) a polynucleotide complementary to the polynucleotide of ii), and v) an RNA equivalent of i)-iv). Alternatively, the target polynucleotide comprises a fragment of a polynucleotide sequence selected from the group consisting of i)-v) above; c) quantifying the amount of hybridization complex; and d) comparing the amount of hybridization complex in the treated biological sample with the amount of hybridization complex in an untreated biological sample, wherein a difference in the amount of hybridization complex in the treated biological sample is indicative of toxicity of the test compound.

BRIEF DESCRIPTION OF THE TABLES

[0171] Table 1 summarizes the nomenclature for the full length polynucleotide and polypeptide sequences of the present invention.

[0172] Table 2 shows the GenBank identification number and annotation of the nearest GenBank homolog for polypeptides of the invention. The probability scores for the matches between each polypeptide and its homolog(s) are also shown.

[0173] Table 3 shows structural features of polypeptide sequences of the invention, including predicted motifs and domains, along with the methods, algorithms, and searchable databases used for analysis of the polypeptides.

[0174] Table 4 lists the cDNA and/or genomic DNA fragments which were used to assemble polynucleotide sequences of the invention, along with selected fragments of the polynucleotide sequences.

[0175] Table 5 shows the representative cDNA library for polynucleotides of the invention.

[0176] Table 6 provides an appendix which describes the tissues and vectors used for construction of the cDNA libraries shown in Table 5.

[0177] Table 7 shows the tools, programs, and algorithms used to analyze the polynucleotides and polypeptides of the invention, along with applicable descriptions, references, and threshold parameters.

[0178] Table 8 shows single nucleotide polymorphisms found in polynucleotide sequences of the invention, along with allele frequencies in different human populations.

DESCRIPTION OF THE INVENTION

[0179] Before the present proteins, nucleotide sequences, and methods are described, it is understood that this invention is not limited to the particular machines, materials and methods described, as these may vary. It is also to be understood that the terminology used herein is for the purpose of describing particular embodiments only, and is not intended to limit the scope of the present invention which will be limited only by the appended claims.

[0180] It must be noted that as used herein and in the appended claims, the singular forms “a,” “an,” and “the” include plural reference unless the context clearly dictates otherwise. Thus, for example, a reference to “a host cell” includes a plurality of such host cells, and a reference to “an antibody” is a reference to one or more antibodies and equivalents thereof known to those skilled in the art, and so forth.

[0181] Unless defined otherwise, all technical and scientific terms used herein have the same meanings as commonly understood by one of ordinary skill in the art to which this invention belongs. Although any machines, materials, and methods similar or equivalent to those described herein can be used to practice or test the present invention, the preferred machines, materials and methods are now described. All publications mentioned herein are cited for the purpose of describing and disclosing the cell lines, protocols, reagents and vectors which are reported in the publications and which might be used in connection with the invention. Nothing herein is to be construed as an admission that the invention is not entitled to antedate such disclosure by virtue of prior invention.

[0182] Definitions

[0183] “CGDD” refers to the amino acid sequences of substantially purified CGDD obtained from any species, particularly a mammalian species, including bovine, ovine, porcine, murine, equine, and human, and from any source, whether natural, synthetic, semi-synthetic, or recombinant.

[0184] The term “agonist” refers to a molecule which intensifies or mimics the biological activity of CGDD. Agonists may include proteins, nucleic acids, carbohydrates, small molecules, or any other compound or composition which modulates the activity of CGDD either by directly interacting with CGDD or by acting on components of the biological pathway in which CGDD participates.

[0185] An “allelic variant” is an alternative form of the gene encoding CGDD. Allelic variants may result from at least one mutation in the nucleic acid sequence and may result in altered mRNAs or in polypeptides whose structure or function may or may not be altered. A gene may have none, one, or many allelic variants of its naturally occurring form. Common mutational changes which give rise to allelic variants are generally ascribed to natural deletions, additions, or substitutions of nucleotides. Each of these types of changes may occur alone, or in combination with the others, one or more times in a given sequence.

[0186] “Altered” nucleic acid sequences encoding CGDD include those sequences with deletions, insertions, or substitutions of different nucleotides, resulting in a polypeptide the same as CGDD or a polypeptide with at least one functional characteristic of CGDD. Included within this definition are polymorphisms which may or may not be readily detectable using a particular oligonucleotide probe of the polynucleotide encoding CGDD, and improper or unexpected hybridization to allelic variants, with a locus other than the normal chromosomal locus for the polynucleotide sequence encoding CGDD. The encoded protein may also be “altered,” and may contain deletions, insertions, or substitutions of amino acid residues which produce a silent change and result in a functionally equivalent CGDD. Deliberate amino acid substitutions may be made on the basis of similarity in polarity, charge, solubility, hydrophobicity, hydrophilicity, and/or the amphipathic nature of the residues, as long as the biological or immunological activity of CGDD is retained. For example, negatively charged amino acids may include aspartic acid and glutamic acid, and positively charged amino acids may include lysine and arginine. Amino acids with uncharged polar side chains having similar hydrophilicity values may include: asparagine and glutamine; and serine and threonine. Amino acids with uncharged side chains having similar hydrophilicity values may include: leucine, isoleucine, and valine; glycine and alanine; and phenylalanine and tyrosine.

[0187] The terms “amino acid” and “amino acid sequence” refer to an oligopeptide, peptide, polypeptide, or protein sequence, or a fragment of any of these, and to naturally occurring or synthetic molecules. Where “amino acid sequence” is recited to refer to a sequence of a naturally occurring protein molecule, “amino acid sequence” and like terms are not meant to limit the amino acid sequence to the complete native amino acid sequence associated with the recited protein molecule.

[0188] “Amplification” relates to the production of additional copies of a nucleic acid sequence. Amplification is generally carried out using polymerase chain reaction (PCR) technologies well known in the art.

[0189] The term “antagonist” refers to a molecule which inhibits or attenuates the biological activity of CGDD. Antagonists may include proteins such as antibodies, nucleic acids, carbohydrates, small molecules, or any other compound or composition which modulates the activity of CGDD either by directly interacting with CGDD or by acting on components of the biological pathway in which CGDD participates.

[0190] The term “antibody” refers to intact immunoglobulin molecules as well as to fragments thereof, such as Fab, F(ab′)₂, and Fv fragments, which are capable of binding an epitopic determinant. Antibodies that bind CGDD polypeptides can be prepared using intact polypeptides or using fragments containing small peptides of interest as the immunizing antigen. The polypeptide or oligopeptide used to immunize an animal (e.g., a mouse, a rat, or a rabbit) can be derived from the translation of RNA, or synthesized chemically, and can be conjugated to a carrier protein if desired. Commonly used carriers that are chemically coupled to peptides include bovine serum albumin, thyroglobulin, and keyhole limpet hemocyanin (KLH). The coupled peptide is then used to immunize the animal.

[0191] The term “antigenic determinant” refers to that region of a molecule (i.e., an epitope) that makes contact with a particular antibody. When a protein or a fragment of a protein is used to immunize a host animal, numerous regions of the protein may induce the production of antibodies which bind specifically to antigenic determinants (particular regions or three-dimensional structures on the protein). An antigenic determinant may compete with the intact antigen (i.e., the immunogen used to elicit the immune response) for binding to an antibody.

[0192] The term “aptamer” refers to a nucleic acid or oligonucleotide molecule that binds to a specific molecular target. Aptamers are derived from an in vitro evolutionary process (e.g., SELEX (Systematic Evolution of Ligands by EXponential Enrichment), described in U.S. Pat. No. 5,270,163), which selects for target-specific aptamer sequences from large combinatorial libraries. Aptamer compositions may be double-stranded or single-stranded, and may include deoxyribonucleotides, ribonucleotides, nucleotide derivatives, or other nucleotide-like molecules. The nucleotide components of an aptamer may have modified sugar groups (e.g., the 2′-OH group of a ribonucleotide may be replaced by 2′-F or 2′-NH₂), which may improve a desired property, e.g., resistance to nucleases or longer lifetime in blood. Aptamers may be conjugated to other molecules, e.g., a high molecular weight carrier to slow clearance of the aptamer from the circulatory system. Aptamers may be specifically cross-linked to their cognate ligands, e.g., by photo-activation of a cross-linker. (See, e.g., Brody, E. N. and L. Gold (2000) J. Biotechnol. 74:5-13.)

[0193] The term “intramer” refers to an aptamer which is expressed in vivo. For example, a vaccinia virus-based RNA expression system has been used to express specific RNA aptamers at high levels in the cytoplasm of leukocytes (Blind, M. et al. (1999) Proc. Natl. Acad. Sci. USA 96:3606-3610).

[0194] The term “spiegelmer” refers to an aptamer which includes L-DNA, L-RNA, or other left-handed nucleotide derivatives or nucleotide-like molecules. Aptamers containing left-handed nucleotides are resistant to degradation by naturally occurring enzymes, which normally act on substrates containing right-handed nucleotides.

[0195] The term “antisense” refers to any composition capable of base-pairing with the “sense” (coding) strand of a specific nucleic acid sequence. Antisense compositions may include DNA; RNA; peptide nucleic acid (PNA); oligonucleotides having modified backbone linkages such as phosphorotioates, methylphosphonates, or benzylphosphonates; oligonucleotides having modified sugar groups such as 2′-methoxyethyl sugars or 2′-methoxyethoxy sugars; or oligonucleotides having modified bases such as 5-methyl cytosine, 2′-deoxyuracil, or 7-deaza-2′-deoxyguanosine. Antisense molecules may be produced by any method including chemical synthesis or transcription. Once introduced into a cell, the complementary antisense molecule base-pairs with a naturally occurring nucleic acid sequence produced by the cell to form duplexes which block either transcription or translation. The designation “negative” or “minus” can refer to the antisense strand, and the designation “positive” or “plus” can refer to the sense strand of a reference DNA molecule.

[0196] The term “biologically active” refers to a protein having structural, regulatory, or biochemical functions of a naturally occurring molecule. Likewise, “immunologically active” or “immunogenic” refers to the capability of the natural, recombinant, or synthetic CGDD, or of any oligopeptide thereof, to induce a specific immune response in appropriate animals or cells and to bind with specific antibodies.

[0197] “Complementary” describes the relationship between two single-stranded nucleic acid sequences that anneal by base-pairing. For example, 5′-AGT-3′ pairs with its complement, 3′-TCA-5′.

[0198] A “composition comprising a given polynucleotide sequence” and a “composition comprising a given amino acid sequence” refer broadly to any composition containing the given polynucleotide or amino acid sequence. The composition may comprise a dry formulation or an aqueous solution. Compositions comprising polynucleotide sequences encoding CGDD or fragments of CGDD may be employed as hybridization probes. The probes may be stored in freeze-dried form and may be associated with a stabilizing agent such as a carbohydrate. In hybridizations, the probe may be deployed in an aqueous solution containing salts (e.g., NaCl), detergents (e.g., sodium dodecyl sulfate; SDS), and other components (e.g., Denhardt's solution, dry milk, salmon sperm DNA, etc.).

[0199] “Consensus sequence” refers to a nucleic acid sequence which has been subjected to repeated DNA sequence analysis to resolve uncalled bases, extended using the XL-PCR kit (Applied Biosystems, Foster City Calif.) in the 5′ and/or the 3′ direction, and resequenced, or which has been assembled from one or more overlapping cDNA, EST, or genomic DNA fragments using a computer program for fragment assembly, such as the GELVIEW fragment assembly system (GCG, Madison Wis.) or Phrap (University of Washington, Seattle Wash.). Some sequences have been both extended and assembled to produce the consensus sequence.

[0200] “Conservative amino acid substitutions” are those substitutions that are predicted to least interfere with the properties of the original protein, i.e., the structure and especially the function of the protein is conserved and not significantly changed by such substitutions. The table below shows amino acids which may be substituted for an original amino acid in a protein and which are regarded as conservative amino acid substitutions. Original Residue Conservative Substitution Ala Gly, Ser Arg His, Lys Asn Asp, Gln, His Asp Asn, Glu Cys Ala, Ser Gln Asn, Glu, His Glu Asp, Gln, His Gly Ala His Asn, Arg, Gln, Glu Ile Leu, Val Leu Ile, Val Lys Arg, Gln, Glu Met Leu, Ile Phe His, Met, Leu, Trp, Tyr Ser Cys, Thr Thr Ser, Val Trp Phe, Tyr Tyr His, Phe, Trp Val Ile, Leu, Thr

[0201] Conservative amino acid substitutions generally maintain (a) the structure of the polypeptide backbone in the area of the substitution, for example, as a beta sheet or alpha helical conformation, (b) the charge or hydrophobicity of the molecule at the site of the substitution, and/or (c) the bulk of the side chain.

[0202] A “deletion” refers to a change in the amino acid or nucleotide sequence that results in the absence of one or more amino acid residues or nucleotides.

[0203] The term “derivative” refers to a chemically modified polynucleotide or polypeptide. Chemical modifications of a polynucleotide can include, for example, replacement of hydrogen by an alkyl, acyl, hydroxyl, or amino group. A derivative polynucleotide encodes a polypeptide which retains at least one biological or immunological function of the natural molecule. A derivative polypeptide is one modified by glycosylation, pegylation, or any similar process that retains at least one biological or immunological function of the polypeptide from which it was derived.

[0204] A “detectable label” refers to a reporter molecule or enzyme that is capable of generating a measurable signal and is covalently or noncovalently joined to a polynucleotide or polypeptide.

[0205] “Differential expression” refers to increased or upregulated; or decreased, downregulated, or absent gene or protein expression, determined by comparing at least two different samples. Such comparisons may be carried out between, for example, a treated and an untreated sample, or a diseased and a normal sample.

[0206] “Exon shuffling” refers to the recombination of different coding regions (exons). Since an exon may represent a structural or functional domain of the encoded protein, new proteins may be assembled through the novel reassortment of stable substructures, thus allowing acceleration of the evolution of new protein functions.

[0207] A “fragment” is a unique portion of CGDD or the polynucleotide encoding CGDD which is identical in sequence to but shorter in length than the parent sequence. A fragment may comprise up to the entire length of the defined sequence, minus one nucleotide/amino acid residue. For example, a fragment may comprise from 5 to 1000 contiguous nucleotides or amino acid residues. A fragment used as a probe, primer, antigen, therapeutic molecule, or for other purposes, may be at least 5, 10, 15, 16, 20, 25, 30, 40, 50, 60, 75, 100, 150, 250 or at least 500 contiguous nucleotides or amino acid residues in length. Fragments may be preferentially selected from certain regions of a molecule. For example, a polypeptide fragment may comprise a certain length of contiguous amino acids selected from the first 250 or 500 amino acids (or first 25% or 50%) of a polypeptide as shown in a certain defined sequence. Clearly these lengths are exemplary, and any length that is supported by the specification, including the Sequence Listing, tables, and figures, may be encompassed by the present embodiments.

[0208] A fragment of SEQ ID NO:22-42 comprises a region of unique polynucleotide sequence that specifically identifies SEQ ID NO:22-42, for example, as distinct from any other sequence in the genome from which the fragment was obtained. A fragment of SEQ ID NO:22-42 is useful, for example, in hybridization and amplification technologies and in analogous methods that distinguish SEQ ID NO:22-42 from related polynucleotide sequences. The precise length of a fragment of SEQ ID NO:22-42 and the region of SEQ ID NO:22-42 to which the fragment corresponds are routinely determinable by one of ordinary skill in the art based on the intended purpose for the fragment.

[0209] A fragment of SEQ ID NO:1-21 is encoded by a fragment of SEQ ID NO:22-42. A fragment of SEQ ID NO:1-21 comprises a region of unique amino acid sequence that specifically identifies SEQ ID NO:1-21. For example, a fragment of SEQ ID NO:1-21 is useful as an immunogenic peptide for the development of antibodies that specifically recognize SEQ ID NO:1-21. The precise length of a fragment of SEQ ID NO:1-21 and the region of SEQ ID NO:1-21 to which the fragment corresponds are routinely determinable by one of ordinary skill in the art based on the intended purpose for the fragment.

[0210] A “full length” polynucleotide sequence is one containing at least a translation initiation codon (e.g., methionine) followed by an open reading frame and a translation termination codon. A “full length” polynucleotide sequence encodes a “full length” polypeptide sequence.

[0211] “Homology” refers to sequence similarity or, interchangeably, sequence identity, between two or more polynucleotide sequences or two or more polypeptide sequences.

[0212] The terms “percent identity” and “% identity,” as applied to polynucleotide sequences, refer to the percentage of residue matches between at least two polynucleotide sequences aligned using a standardized algorithm. Such an algorithm may insert, in a standardized and reproducible way, gaps in the sequences being compared in order to optimize alignment between two sequences, and therefore achieve a more meaningful comparison of the two sequences.

[0213] Percent identity between polynucleotide sequences may be determined using the default parameters of the CLUSTAL V algorithm as incorporated into the MEGALIGN version 3.12e sequence alignment program. This program is part of the LASERGENE software package, a suite of molecular biological analysis programs (DNASTAR, Madison Wis.). CLUSTAL V is described in Higgins, D. G. and P. M. Sharp (1989) CABIOS 5:151-153 and in Higgins, D. G. et al. (1992) CABIOS 8:189-191. For pairwise alignments of polynucleotide sequences, the default parameters are set as follows: Ktuple=2, gap penalty=5, window=4, and “diagonals saved”=4. The “weighted” residue weight table is selected as the default. Percent identity is reported by CLUSTAL V as the “percent similarity” between aligned polynucleotide sequences.

[0214] Alternatively, a suite of commonly used and freely available sequence comparison algorithms is provided by the National Center for Biotechnology Information (NCBI) Basic Local Alignment Search Tool (BLAST) (Altschul, S. F. et al. (1990) J. Mol. Biol. 215:403-410), which is available from several sources, including the NCBI, Bethesda, Md., and on the Internet at http://www.ncbi.nlm.nih.gov/BLAST/. The BLAST software suite includes various sequence analysis programs including “blastn,” that is used to align a known polynucleotide sequence with other polynucleotide sequences from a variety of databases. Also available is a tool called “BLAST 2 Sequences” that is used for direct pairwise comparison of two nucleotide sequences. “BLAST 2 Sequences” can be accessed and used interactively at http://www.ncbi.nlm.nih.gov/gorf/bl2.html. The “BLAST 2 Sequences” tool can be used for both blastn and blastp (discussed below). BLAST programs are commonly used with gap and other parameters set to default settings. For example, to compare two nucleotide sequences, one may use blastn with the “BLAST 2 Sequences” tool Version 2.0.12 (Apr. 21, 2000) set at default parameters. Such default parameters may be, for example:

[0215] Matrix: BLOSUM62

[0216] Reward for match: 1

[0217] Penalty for mismatch: −2

[0218] Open Gap: 5 and Extension Gap: 2 penalties

[0219] Gap x drop-off 50

[0220] Expect: 10

[0221] Word Size: 11

[0222] Filter: on

[0223] Percent identity may be measured over the length of an entire defined sequence, for example, as defined by a particular SEQ ID number, or may be measured over a shorter length, for example, over the length of a fragment taken from a larger, defined sequence, for instance, a fragment of at least 20, at least 30, at least 40, at least 50, at least 70, at least 100′ or at least 200 contiguous nucleotides. Such lengths are exemplary only, and it is understood that any fragment length supported by the sequences shown herein, in the tables, figures, or Sequence Listing, may be used to describe a length over which percentage identity may be measured.

[0224] Nucleic acid sequences that do not show a high degree of identity may nevertheless encode similar amino acid sequences due to the degeneracy of the genetic code. It is understood that changes in a nucleic acid sequence can be made using this degeneracy to produce multiple nucleic acid sequences that all encode substantially the same protein.

[0225] The phrases “percent identity” and “% identity,” as applied to polypeptide sequences, refer to the percentage of residue matches between at least two polypeptide sequences aligned using a standardized algorithm. Methods of polypeptide sequence alignment are well-known. Some alignment methods take into account conservative amino acid substitutions. Such conservative substitutions, explained in more detail above, generally preserve the charge and hydrophobicity at the site of substitution, thus preserving the structure (and therefore function) of the polypeptide.

[0226] Percent identity between polypeptide sequences may be determined using the default parameters of the CLUSTAL V algorithm as incorporated into the MEGALIGN version 3.12e sequence alignment program (described and referenced above). For pairwise alignments of polypeptide sequences using CLUSTAL V, the default parameters are set as follows: Ktuple=1, gap penalty=3, window=5, and “diagonals saved”=5. The PAM250 matrix is selected as the default residue weight table. As with polynucleotide alignments, the percent identity is reported by CLUSTAL V as the “percent similarity” between aligned polypeptide sequence pairs.

[0227] Alternatively the NCBI BLAST software suite may be used. For example, for a pairwise comparison of two polypeptide sequences, one may use the “BLAST 2 Sequences” tool Version 2.0.12 (Apr. 21, 2000) with blastp set at default parameters. Such default parameters may be, for example:

[0228] Matrix: BLOSUM162

[0229] Open Gap: 11 and Extension Gap: 1 penalties

[0230] Gap x drop-off 50

[0231] Expect: 10

[0232] Word Size: 3

[0233] Filter: on

[0234] Percent identity may be measured over the length of an entire defined polypeptide sequence, for example, as defined by a particular SEQ D number, or may be measured over a shorter length, for example, over the length of a fragment taken from a larger, defined polypeptide sequence, for instance, a fragment of at least 15, at least 20, at least 30, at least 40, at least 50, at least 70 or at least 150 contiguous residues. Such lengths are exemplary only, and it is understood that any fragment length supported by the sequences shown herein, in the tables, figures or Sequence Listing, may be used to describe a length over which percentage identity may be measured.

[0235] “Human artificial chromosomes” (HACs) are linear microchromosomes which may contain DNA sequences of about 6 kb to 10 Mb in size and which contain all of the elements required for chromosome replication, segregation and maintenance.

[0236] The term “humanized antibody” refers to an antibody molecule in which the amino acid sequence in the non-antigen binding regions has been altered so that the antibody more closely resembles a human antibody, and still retains its original binding ability.

[0237] “Hybridization” refers to the process by which a polynucleotide strand anneals with a complementary strand through base pairing under defined hybridization conditions. Specific hybridization is an indication that two nucleic acid sequences share a high degree of complementarity. Specific hybridization complexes form under permissive annealing conditions and remain hybridized after the “washing” step(s). The washing step(s) is particularly important in determining the stringency of the hybridization process, with more stringent conditions allowing less non-specific binding, i.e., binding between pairs of nucleic acid strands that are not perfectly matched. Permissive conditions for annealing of nucleic acid sequences are routinely determinable by one of ordinary skill in the art and may be consistent among hybridization experiments, whereas wash conditions may be varied among experiments to achieve the desired stringency, and therefore hybridization specificity. Permissive annealing conditions occur, for example, at 68° C. in the presence of about 6×SSC, about 1% (w/v) SDS, and about 100 μg/ml sheared, denatured salmon sperm DNA.

[0238] Generally, stringency of hybridization is expressed, in part, with reference to the temperature under which the wash step is carried out. Such wash temperatures are typically selected to be about 5° C. to 20° C. lower than the thermal melting point (T_(m)) for the specific sequence at a defined ionic strength and pH. The T_(m) is the temperature (under defined ionic strength and pH) at which 50% of the target sequence hybridizes to a perfectly matched probe. An equation for calculating T_(m) and conditions for nucleic acid hybridization are well known and can be found in Sambrook, J. et al. (1989) Molecular Cloning: A Laboratory Manual, 2^(nd) ed., vol. 1-3, Cold Spring Harbor Press, Plainview N.Y.; specifically see volume 2, chapter 9.

[0239] High stringency conditions for hybridization between polynucleotides of the present invention include wash conditions of 68° C. in the presence of about 0.2×SSC and about 0.1% SDS, for 1 hour. Alternatively, temperatures of about 65° C., 60° C., 55° C., or 42° C. may be used. SSC concentration may be varied from about 0.1 to 2×SSC, with SDS being present at about 0.1%. Typically, blocking reagents are used to block non-specific hybridization. Such blocking reagents include, for instance, sheared and denatured salmon sperm DNA at about 100-200 μg/ml. Organic solvent, such as formamide at a concentration of about 35-50% v/v, may also be used under particular circumstances, such as for RNA:DNA hybridizations. Useful variations on these wash conditions will be readily apparent to those of ordinary skill in the art. Hybridization, particularly under high stringency conditions, may be suggestive of evolutionary similarity between the nucleotides. Such similarity is strongly indicative of a similar role for the nucleotides and their encoded polypeptides.

[0240] The term “hybridization complex” refers to a complex formed between two nucleic acid sequences by virtue of the formation of hydrogen bonds between complementary bases. A hybridization complex may be formed in solution (e.g., C₀t or R₀t analysis) or formed between one nucleic acid sequence present in solution and another nucleic acid sequence immobilized on a solid support (e.g., paper, membranes, filters, chips, pins or glass slides, or any other appropriate substrate to which cells or their nucleic acids have been fixed).

[0241] The words “insertion” and “addition” refer to changes in an amino acid or nucleotide sequence resulting in the addition of one or more amino acid residues or nucleotides, respectively.

[0242] “Immune response” can refer to conditions associated with inflammation, trauma, immune disorders, or infectious or genetic disease, etc. These conditions can be characterized by expression of various factors, e.g., cytokines, chemokines, and other signaling molecules, which may affect cellular and systemic defense systems.

[0243] An “immunogenic fragment” is a polypeptide or oligopeptide fragment of CGDD which is capable of eliciting an immune response when introduced into a living organism, for example, a mammal. The term “immunogenic fragment” also includes any polypeptide or oligopeptide fragment of CGDD which is useful in any of the antibody production methods disclosed herein or known in the art.

[0244] The term “microarray” refers to an arrangement of a plurality of polynucleotides, polypeptides, or other chemical compounds on a substrate.

[0245] The terms “element” and “array element” refer to a polynucleotide, polypeptide, or other chemical compound having a unique and defined position on a microarray.

[0246] The term “modulate” refers to a change in the activity of CGDD. For example, modulation may cause an increase or a decrease in protein activity, binding characteristics, or any other biological, functional, or immunological properties of CGDD.

[0247] The phrases “nucleic acid” and “nucleic acid sequence” refer to a nucleotide, oligonucleotide, polynucleotide, or any fragment thereof. These phrases also refer to DNA or RNA of genomic or synthetic origin which may be single-stranded or double-stranded and may represent the sense or the antisense strand, to peptide nucleic acid (PNA), or to any DNA-like or RNA-like material.

[0248] “Operably linked” refers to the situation in which a first nucleic acid sequence is placed in a functional relationship with a second nucleic acid sequence. For instance, a promoter is operably linked to a coding sequence if the promoter affects the transcription or expression of the coding sequence. Operably linked DNA sequences may be in close proximity or contiguous and, where necessary to join two protein coding regions, in the same reading frame.

[0249] “Peptide nucleic acid” (PNA) refers to an antisense molecule or anti-gene agent which comprises an oligonucleotide of at least about 5 nucleotides in length linked to a peptide backbone of amino acid residues ending in lysine. The terminal lysine confers solubility to the composition. PNAs preferentially bind complementary single stranded DNA or RNA and stop transcript elongation, and may be pegylated to extend their lifespan in the cell.

[0250] “Post-translational modification” of an CGDD may involve lipidation, glycosylation, phosphorylation, acetylation, racemization, proteolytic cleavage, and other modifications known in the art. These processes may occur synthetically or biochemically. Biochemical modifications will vary by cell type depending on the enzymatic milieu of CGDD.

[0251] “Probe” refers to nucleic acid sequences encoding CGDD, their complements, or fragments thereof, which are used to detect identical, allelic or related nucleic acid sequences. Probes are isolated oligonucleotides or polynucleotides attached to a detectable label or reporter molecule. Typical labels include radioactive isotopes, ligands, chemiluminescent agents, and enzymes. “Primers” are short nucleic acids, usually DNA oligonucleotides, which may be annealed to a target polynucleotide by complementary base-pairing. The primer may then be extended along the target DNA strand by a DNA polymerase enzyme. Primer pairs can be used for amplification (and identification) of a nucleic acid sequence, e.g., by the polymerase chain reaction (PCR).

[0252] Probes and primers as used in the present invention typically comprise at least 15 contiguous nucleotides of a known sequence. In order to enhance specificity, longer probes and primers may also be employed, such as probes and primers that comprise at least 20, 25, 30, 40, 50, 60, 70, 80, 90, 100, or at least 150 consecutive nucleotides of the disclosed nucleic acid sequences. Probes and primers may be considerably longer than these examples, and it is understood that any length supported by the specification, including the tables, figures, and Sequence Listing, may be used.

[0253] Methods for preparing and using probes and primers are described in the references, for example Sambrook, J: et al. (1989) Molecular Cloning: A Laboratory Manual, 2^(nd) ed., vol. 1-3, Cold Spring Harbor Press, Plainview N.Y.; Ausubel, F. M. et al. (1987) Current Protocols in Molecular Biology, Greene Publ. Assoc. & Wiley-Intersciences, New York N.Y.; Innis, M. et al. (1990) PCR Protocols, A Guide to Methods and Applications, Academic Press, San Diego Calif. PCR primer pairs can be derived from a known sequence, for example, by using computer programs intended for that purpose such as Primer (Version 0.5, 1991, Whitehead Institute for Biomedical Research, Cambridge Mass.).

[0254] Oligonucleotides for use as primers are selected using software known in the art for such purpose. For example, OLIGO 4.06 software is useful for the selection of PCR primer pairs of up to 100 nucleotides each, and for the analysis of oligonucleotides and larger polynucleotides of up to 5,000 nucleotides from an input polynucleotide sequence of up to 32 kilobases. Similar primer selection programs have incorporated additional features for expanded capabilities. For example, the PrimOU primer selection program (available to the public from the Genome Center at University of Texas South West Medical Center, Dallas Tex.) is capable of choosing specific primers from megabase sequences and is thus useful for designing primers on a genome-wide scope. The Primer3 primer selection program (available to the public from the Whitehead Institute/MIT Center for Genome Research, Cambridge Mass.) allows the user to input a “mispriming library,” in which sequences to avoid as primer binding sites are user-specified. Primer3 is useful, in particular, for the selection of oligonucleotides for microarrays. (The source code for the latter two primer selection programs may also be obtained from their respective sources and modified to meet the user's specific needs.) The PrimeGen program (available to the public from the UK Human Genome Mapping Project Resource Centre, Cambridge UK) designs primers based on multiple sequence alignments, thereby allowing selection of primers that hybridize to either the most conserved or least conserved regions of aligned nucleic acid sequences. Hence, this program is useful for identification of both unique and conserved oligonucleotides and polynucleotide fragments. The oligonucleotides and polynucleotide fragments identified by any of the above selection methods are useful in hybridization technologies, for example, as PCR or sequencing primers, microarray elements, or specific probes to identify fully or partially complementary polynucleotides in a sample of nucleic acids. Methods of oligonucleotide selection are not limited to those described above.

[0255] A “recombinant nucleic acid” is a sequence that is not naturally occurring or has a sequence that is made by an artificial combination of two or more otherwise separated segments of sequence. This artificial combination is often accomplished by chemical synthesis or, more commonly, by the artificial manipulation of isolated segments of nucleic acids, e.g., by genetic engineering techniques such as those described in Sambrook, supra. The term recombinant includes nucleic acids that have been altered solely by addition, substitution, or deletion of a portion of the nucleic acid. Frequently, a recombinant nucleic acid may include a nucleic acid sequence operably linked to a promoter sequence. Such a recombinant nucleic acid may be part of a vector that is used, for example, to transform a cell.

[0256] Alternatively, such recombinant nucleic acids may be part of a viral vector, e.g., based on a vaccinia virus, that could be use to vaccinate a mammal wherein the recombinant nucleic acid is expressed, inducing a protective immunological response in the mammal.

[0257] A “regulatory element” refers to a nucleic acid sequence usually derived from untranslated regions of a gene and includes enhancers, promoters, introns, and 5′ and 3′ untranslated regions (UTRs). Regulatory elements interact with host or viral proteins which control transcription, translation, or RNA stability.

[0258] “Reporter molecules” are chemical or biochemical moieties used for labeling a nucleic acid, amino acid, or antibody. Reporter molecules include radionuclides; enzymes; fluorescent, chemiluminescent, or chromogenic agents; substrates; cofactors; inhibitors; magnetic particles; and other moieties known in the art.

[0259] An “RNA equivalent,” in reference to a DNA sequence, is composed of the same linear sequence of nucleotides as the reference DNA sequence with the exception that all occurrences of the nitrogenous base thymine are replaced with uracil, and the sugar backbone is composed of ribose instead of deoxyribose.

[0260] The term “sample” is used in its broadest sense. A sample suspected of containing CGDD, nucleic acids encoding CGDD, or fragments thereof may comprise a bodily fluid; an extract from a cell, chromosome, organelle, or membrane isolated from a cell; a cell; genomic DNA, RNA, or cDNA, in solution or bound to a substrate; a tissue; a tissue print; etc.

[0261] The terms “specific binding” and “specifically binding” refer to that interaction between a protein or peptide and an agonist, an antibody, an antagonist, a small molecule, or any natural or synthetic binding composition. The interaction is dependent upon the presence of a particular structure of the protein, e.g., the antigenic determinant or epitope, recognized by the binding molecule. For example, if an antibody is specific for epitope “A,” the presence of a polypeptide comprising the epitope A, or the presence of free unlabeled A, in a reaction containing free labeled A and the antibody will reduce the amount of labeled A that binds to the antibody.

[0262] The term “substantially purified” refers to nucleic acid or amino acid sequences that are removed from their natural environment and are isolated or separated, and are at least 60% free, preferably at least 75% free, and most preferably at least 90% free from other components with which they are naturally associated.

[0263] A “substitution” refers to the replacement of one or more amino acid residues or nucleotides by different amino acid residues or nucleotides, respectively.

[0264] “Substrate” refers to any suitable rigid or semi-rigid support including membranes, filters, chips, slides, wafers, fibers, magnetic or nonmagnetic beads, gels, tubing, plates, polymers, microparticles and capillaries. The substrate can have a variety of surface forms, such as wells, trenches, pins, channels and pores, to which polynucleotides or polypeptides are bound.

[0265] A “transcript image” or “expression profile” refers to the collective pattern of gene expression by a particular cell type or tissue under given conditions at a given time.

[0266] “Transformation” describes a process by which exogenous DNA is introduced into a recipient cell. Transformation may occur under natural or artificial conditions according to various methods well known in the art, and may rely on any known method for the insertion of foreign nucleic acid sequences into a prokaryotic or eukaryotic host cell. The method for transformation is selected based on the type of host cell being transformed and may include, but is not limited to, bacteriophage or viral infection, electroporation, heat shock, lipofection, and particle bombardment. The term “transformed cells” includes stably transformed cells in which the inserted DNA is capable of replication either as an autonomously replicating plasmid or as part of the host chromosome, as well as transiently transformed cells which express the inserted DNA or RNA for limited periods of time.

[0267] A “transgenic organism,” as used herein, is any organism, including but not limited to animals and plants, in which one or more of the cells of the organism contains heterologous nucleic acid introduced by way of human intervention, such as by transgenic techniques well known in the art. The nucleic acid is introduced into the cell, directly or indirectly by introduction into a precursor of the cell, by way of deliberate genetic manipulation, such as by microinjection or by infection with a recombinant virus. In one alternative, the nucleic acid can be introduced by infection with a recombinant viral vector, such as a lentiviral vector (Lois, C. et al. (2002) Science 295:868-872). The term genetic manipulation does not include classical cross-breeding, or in vitro fertilization, but rather is directed to the introduction of a recombinant DNA molecule. The transgenic organisms contemplated in accordance with the present invention include bacteria, cyanobacteria, fungi, plants and animals. The isolated DNA of the present invention can be introduced into the host by methods known in the art, for example infection, transfection, transformation or transconjugation. Techniques for transferring the DNA of the present invention into such organisms are widely known and provided in references such as Sambrook et al. (1989), supra.

[0268] A “variant” of a particular nucleic acid sequence is defined as a nucleic acid sequence having at least 40% sequence identity to the particular nucleic acid sequence over a certain length of one of the nucleic acid sequences using blastn with the “BLAST 2 Sequences” tool Version 2.0.9 (May 7, 1999) set at default parameters. Such a pair of nucleic acids may show, for example, at least 50%, at least 60%, at least 70%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% or greater sequence identity over a certain defined length. A variant may be described as, for example, an “allelic” (as defined above), “splice,” “species,” or “polymorphic” variant. A splice variant may have significant identity to a reference molecule, but will generally have a greater or lesser number of polynucleotides due to alternate splicing of exons during mRNA processing. The corresponding polypeptide may possess additional functional domains or lack domains that are present in the reference molecule. Species variants are polynucleotide sequences that vary from one species to another. The resulting polypeptides will generally have significant amino acid identity relative to each other. A polymorphic variant is a variation in the polynucleotide sequence of a particular gene between individuals of a given species. Polymorphic variants also may encompass “single nucleotide polymorphisms” (SNPs) in which the polynucleotide sequence varies by one nucleotide base. The presence of SNPs may be indicative of, for example, a certain population, a disease state, or a propensity for a disease state.

[0269] A “variant” of a particular polypeptide sequence is defined as a polypeptide sequence having at least 40% sequence identity to the particular polypeptide sequence over a certain length of one of the polypeptide sequences using blastp with the “BLAST 2 Sequences” tool Version 2.0.9 (May-07-1999) set at default parameters. Such a pair of polypeptides may show, for example, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% or greater sequence identity over a certain defined length of one of the polypeptides.

[0270] The Invention

[0271] The invention is based on the discovery of new human proteins associated with cell growth, differentiation, and death (CGDD), the polynucleotides encoding CGDD, and the use of these compositions for the diagnosis, treatment, or prevention of cell proliferative disorders including cancer, developmental disorders, neurological disorders, autoimmune/inflammatory disorders, reproductive disorders, and disorders of the placenta.

[0272] Table 1 summarizes the nomenclature for the full length polynucleotide and polypeptide sequences of the invention. Each polynucleotide and its corresponding polypeptide are correlated to a single Incyte project identification number (Incyte Project ID). Each polypeptide sequence is denoted by both a polypeptide sequence identification number (Polypeptide SEQ ID NO:) and an Incyte polypeptide sequence number (Incyte Polypeptide ID) as shown. Each polynucleotide sequence is denoted by both a polynucleotide sequence identification number (Polynucleotide SEQ ID NO:) and an Incyte polynucleotide consensus sequence number (Incyte Polynucleotide ID) as shown.

[0273] Table 2 shows sequences with homology to the polypeptides of the invention as identified by BLAST analysis against the GenBank protein (genpept) database. Columns 1 and 2 show the polypeptide sequence identification number (Polypeptide SEQ ID NO:) and the corresponding Incyte polypeptide sequence number (Incyte Polypeptide ID) for polypeptides of the invention. Column 3 shows the GenBank identification number (GenBank ID NO:) of the nearest GenBank homolog. Column 4 shows the probability scores for the matches between each polypeptide and its homolog(s). Column 5 shows the annotation of the GenBank homolog(s), along with relevant citations where applicable, all of which are expressly incorporated by reference herein.

[0274] Table 3 shows various structural features of the polypeptides of the invention. Columns 1 and 2 show the polypeptide sequence identification number (SEQ ID NO:) and the corresponding Incyte polypeptide sequence number (Incyte Polypeptide ID) for each polypeptide of the invention. Column 3 shows the number of amino acid residues in each polypeptide. Column 4 shows potential phosphorylation sites, and column 5 shows potential glycosylation sites, as determined by the MOTIFS program of the GCG sequence analysis software package (Genetics Computer Group, Madison Wis.). Column 6 shows amino acid residues comprising signature sequences, domains, and motifs. Column 7 shows analytical methods for protein structure/function analysis and in some cases, searchable databases to which the analytical methods were applied.

[0275] Together, Tables 2 and 3 summarize the properties of polypeptides of the invention, and these properties establish that the claimed polypeptides are proteins associated with cell growth, differentiation, and death.

[0276] For example, SEQ ID NO:1 is 92% identical, from residue M1 to residue L1738, to murine ubiquitin-protein ligase E3-alpha (GenBank ID g3170887) as determined by the Basic Local Alignment Search Tool (BLAST). (See Table 2.) The BLAST probability score is 0.0, which indicates the probability of obtaining the observed polypeptide sequence alignment by chance. SEQ ID NO:1 also contains a putative zinc finger in N-recognin domain as determined by searching for statistically significant matches in the hidden Markov model (HMM)-based PFAM database of conserved protein family domains. (See Table 3.) Data from additional BLAST analyses provide further corroborative evidence that SEQ ID NO:1 is an ubiquitin protein ligase.

[0277] In an alternative example, For example, SEQ ID NO:3 is 88% identical, from residue M1 to residue D854, to murine ubiquitin-protein ligase Nedd4-2 (GenBank ID g12656270) as determined by the Basic Local Alignment Search Tool (BLAST). (See Table 2.) The BLAST probability score is 0.0, which indicates the probability of obtaining the observed polypeptide sequence alignment by chance. SEQ ID NO:3 also contains HECT (ubiquitin-transferase) and WW domains determined by searching for statistically significant matches in the hidden Markov model (HMM)-based PFAM database of conserved protein family domains. (See Table 3.) Data from BLIMPS and MOTIFS analyses provide further corroborative evidence that SEQ ID NO:3 is an ubiquitin-protein ligase.

[0278] In an alternative example, SEQ ID NO:5 is 100% identical, from residue M27 to residue D538, to human cisplatin resistance related protein CRR9p (GenBank ID g12248402) as determined by the Basic Local Alignment Search Tool (BLAST). (See Table 2.) The BLAST probability score is 8.4e−281, which indicates the probability of obtaining the observed polypeptide sequence alignment by chance. Data from additional BLAST analyses provide further corroborative evidence that SEQ ID NO:5 is an apoptosis-associated protein.

[0279] In an alternative example, SEQ ID NO:9 is 80% identical, from residue M1 to residue S710, to mouse RalGDS-like protein 3 (GenBank ID g8650435) as determined by the Basic Local Alignment Search Tool (BLAST). (See Table 2.) The BLAST probability score is 1.5e−299, which indicates the probability of obtaining the observed polypeptide sequence alignment by chance. SEQ ID NO:9 also contains a Ras association (RalGDS/AF-6) domain and a RasGEF domain as determined by searching for statistically significant matches in the hidden Markov model (HMM)-based PFAM database of conserved protein family domains. (See Table 3.) Data from additional BLAST analyses using the PRODOM and DOMO databases provide further corroborative evidence that SEQ ID NO:9 is a guanine nucleotide dissociation factor.

[0280] In an alternative example, SEQ ID NO:12 is 77% identical, from residue A64 to residue Y365 and 100% identical from residue M1 to D109, to Sgt1 (GenBank ID g4809026) as determined by the Basic Local Alignment Search Tool (BLAST). (See Table 2.) The BLAST probability score is 3.2e−121, which indicates the probability of obtaining the observed polypeptide sequence alignment by chance. SEQ ID NO: 12 also contains tetratricopeptide (TPR) domains from residue A45 to N78 and from residue S79 to T112, as determined by searching for statistically significant matches in the hidden Markov model (HMM)-based PFAM database of conserved protein family domains. (See Table 3.) TPR repeats are believed to mediate protein-protein interactions and are found in a number of proteins involved in mitosis. In addition, SPSCAN identifies a potential signal peptide from residue M1 through A68.

[0281] In an alternative example, SEQ ID NO:13 is 100% identical, from residue M1 to residue K365, to human proto-oncogene Wnt-5A (GenBank ID g348918) as determined by the Basic Local Alignment Search Tool (BLAST). (See Table 2.) The BLAST probability score is 2.5e−205, which indicates the probability of obtaining the observed polypeptide sequence alignment by chance. SEQ ID NO:13 also contains a wnt-1 family domain as determined by searching for statistically significant matches in the hidden Markov model (HMM)-based PFAM database of conserved protein family domains. (See Table 3.) Data from BLIMS, MOTIFS, and PROFILESCAN analyses provide further corroborative evidence that SEQ ID NO:13 is a wnt-1 family protein, a member of the wnt family of secreted glycoproteins.

[0282] In an alternative example, SEQ ID NO:16 is 50% identical, from residue A18 to residue F1014, to human cyclin-E binding protein 1 (GenBank ID g6630609) as determined by the Basic Local Alignment Search Tool (BLAST). (See Table 2.) The BLAST probability score is 3.6e−252, which indicates the probability of obtaining the observed polypeptide sequence alignment by chance. SEQ ID NO:16 also contains a HECT (ubiquitin transferase) domain, and a regulator of chromosome condensation (RCC1) protein doomain as determined by searching for statistically significant matches in the hidden Markov model (HMM)-based PFAM database of conserved protein family domains. (See Table 3.) Data from BLIMPS, MOTIFS, and PROFILESCAN analyses provide further corroborative evidence that SEQ ID NO:16 is a cyclin-binding protein.

[0283] In an alternative example, SEQ ID NO:17 is 99% identical, from residue M1 to residue S1462, to a human cyclophilin-related protein (GenBank ID g5923891) as determined by the Basic Local Alignment Search Tool (BLAST). (See Table 2.) The BLAST probability score is 0.0, which indicates the probability of obtaining the observed polypeptide sequence alignment by chance. SEQ ID NO:17 also contains a cyclophilin-type peptidyl-prolyl cis-trans isomerase domain as determined by searching for statistically significant matches in the hidden Markov model (HMM)-based PFAM database of conserved protein family domains. (See Table 3.) Data from BLIMPS, MOTIFS, and PROFILESCAN analyses provide further corroborative evidence that SEQ ID NO:17 is a cyclophilin-related protein.

[0284] In an alternative example, SEQ ID NO:19 is 34% identical, from residue K3 to residue S175, and 26% identical, from residue R40 to Q327, to human apoptotic protease activating factor 1 (GenBank ID g2330015) as determined by the Basic Local Alignment Search Tool (BLAST). (See Table 2.) The BLAST probability score is 8.3e−21, which indicates the probability of obtaining the observed polypeptide sequence alignment by chance. SEQ ID NO:19 also contains a SAM domain and G-protein beta WD-40 repeats as determined by searching for statistically significant matches in the hidden Markov model (HMM)-based PFAM database of conserved protein family domains. (See Table 3.) Data from BLIMPS, MOTIFS, and PROFILESCAN analyses provide further corroborative evidence that SEQ ID NO:19 contains multiple beta G-protein WD-40 signatures similarly to Apaf-1. SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6-8, SEQ ID NO:10-11, SEQ ID NO:14-15, SEQ ID NO:18, and SEQ ID NO:20-21 were analyzed and annotated in a similar manner. The algorithms and parameters for the analysis of SEQ ID NO:1-21 are described in Table 7.

[0285] As shown in Table 4, the full length polynucleotide sequences of the present invention were assembled using cDNA sequences or coding (exon) sequences derived from genomic DNA, or any combination of these two types of sequences. Column 1 lists the polynucleotide sequence identification number (Polynucleotide SEQ ID NO:), the corresponding Incyte polynucleotide consensus sequence number (Incyte ID) for each polynucleotide of the invention, and the length of each polynucleotide sequence in basepairs. Column 2 shows the nucleotide start (5′) and stop (3′) positions of the cDNA and/or genomic sequences used to assemble the full length polynucleotide sequences of the invention, and of fragments of the polynucleotide sequences which are useful, for example, in hybridization or amplification technologies that identify SEQ ID NO:22-42 or that distinguish between SEQ ID NO:22-42 and related polynucleotide sequences.

[0286] The polynucleotide fragments described in Column 2 of Table 4 may refer specifically, for example, to Incyte cDNAs derived from tissue-specific cDNA libraries or from pooled cDNA libraries. Alternatively, the polynucleotide fragments described in column 2 may refer to GenBank cDNAs or ESTs which contributed to the assembly of the full length polynucleotide sequences. In addition, the polynucleotide fragments described in column 2 may identify sequences derived from the ENSEMBL (The Sanger Centre, Cambridge, UK) database (i.e., those sequences including the designation “ENST”). Alternatively, the polynucleotide fragments described in column 2 may be derived from the NCBI RefSeq Nucleotide Sequence Records Database (i.e., those sequences including the designation “NM” or “NT”) or the NCBI RefSeq Protein Sequence Records (i.e., those sequences including the designation “NP”). Alternatively, the polynucleotide fragments described in column 2 may refer to assemblages of both cDNA and Genscan-predicted exons brought together by an “exon stitching” algorithm. For example, a polynucleotide sequence identified as FL_XXXXXX_N₁ _(—) N₂ _(—) YYYYY_N₃ _(—) N₄ represents a “stitched” sequence in which XXXXXX is the identification number of the cluster of sequences to which the algorithm was applied, and YYYYY is the number of the prediction generated by the algorithm, and N_(1,2,3) . . . , if present, represent specific exons that may have been manually edited during analysis (See Example V). Alternatively, the polynucleotide fragments in column 2 may refer to assemblages of exons brought together by an “exon-stretching” algorithm. For example, a polynucleotide sequence identified as FL_XXXXXX_gAAAAA_gBBBBB_(—)1_N is a “stretched” sequence, with XXXXXX being the Incyte project identification number, gAAAAA being the GenBank identification number of the human genomic sequence to which the “exon-stretching” algorithm was applied, gBBBBB being the GenBank identification number or NCBI RefSeq identification number of the nearest GenBank protein homolog, and N referring to specific exons (See Example V). In instances where a RefSeq sequence was used as a protein homolog for the “exon-stretching” algorithm, a RefSeq identifier (denoted by “NM,” “NP,” or “NT”) maybe used in place of the GenBank identifier (i.e., gBBBBB).

[0287] Alternatively, a prefix identifies component sequences that were hand-edited, predicted from genomic DNA sequences, or derived from a combination of sequence analysis methods. The following Table lists examples of component sequence prefixes and corresponding sequence analysis methods associated with the prefixes (see Example IV and Example V). Prefix Type of analysis and/or examples of programs GNN, Exon prediction from genomic sequences using, for example, GFG, GENSCAN (Stanford University, CA, USA) or FGENES ENST (Computer Genomics Group, The Sanger Centre, Cambridge, UK). GBI Hand-edited analysis of genomic sequences. FL Stitched or stretched genomic sequences (see Example V). INCY Full length transcript and exon prediction from mapping of EST sequences to the genome. Genomic location and EST composition data are combined to predict the exons and resulting transcript.

[0288] In some cases, Incyte cDNA coverage redundant with the sequence coverage shown in Table 4 was obtained to confirm the final consensus polynucleotide sequence, but the relevant Incyte cDNA identification numbers are not shown.

[0289] Table 5 shows the representative cDNA libraries for those full length polynucleotide sequences which were assembled using Incyte cDNA sequences. The representative cDNA library is the Incyte cDNA library which is most frequently represented by the Incyte cDNA sequences which were used to assemble and confirm the above polynucleotide sequences. The tissues and vectors which were used to construct the cDNA libraries shown in Table 5 are described in Table 6.

[0290] The invention also encompasses CGDD variants. A preferred CGDD variant is one which has at least about 80%, or alternatively at least about 90%, or even at least about 95% amino acid sequence identity to the CGDD amino acid sequence, and which contains at least one functional or structural characteristic of CGDD.

[0291] The invention also encompasses polynucleotides which encode CGDD. In a particular embodiment, the invention encompasses a polynucleotide sequence comprising a sequence selected from the group consisting of SEQ ID NO:22-42, which encodes CGDD. The polynucleotide sequences of SEQ ID NO:22-42, as presented in the Sequence Listing, embrace the equivalent RNA sequences, wherein occurrences of the nitrogenous base thymine are replaced with uracil, and the sugar backbone is composed of ribose instead of deoxyribose.

[0292] The invention also encompasses a variant of a polynucleotide sequence encoding CGDD. In particular, such a variant polynucleotide sequence will have at least about 70%, or alternatively at least about 85%, or even at least about 95% polynucleotide sequence identity to the polynucleotide sequence encoding CGDD. A particular aspect of the invention encompasses a variant of a polynucleotide sequence comprising a sequence selected from the group consisting of SEQ ID NO:22-42 which has at least about 70%, or alternatively at least about 85%, or even at least about 95% polynucleotide sequence identity to a nucleic acid sequence selected from the group consisting of SEQ ID NO:22-42. Any one of the polynucleotide variants described above can encode an amino acid sequence which contains at least one functional or structural characteristic of CGDD.

[0293] In addition, or in the alternative, a polynucleotide variant of the invention is a splice variant of a polynucleotide sequence encoding CGDD. A splice variant may have portions which have significant sequence identity to the polynucleotide sequence encoding CGDD, but will generally have a greater or lesser number of polynucleotides due to additions or deletions of blocks of sequence arising from alternate splicing of exons during mRNA processing. A splice variant may have less than about 70%, or alternatively less than about 60%, or alternatively less than about 50% polynucleotide sequence identity to the polynucleotide sequence encoding CGDD over its entire length; however, portions of the splice variant will have at least about 70%, or alternatively at least about 85%, or alternatively at least about 95%, or alternatively 100% polynucleotide sequence identity to portions of the polynucleotide sequence encoding CGDD. For example, a polynucleotide comprising a sequence of SEQ ID NO:42 is a splice variant of a polynucleotide comprising a sequence of SEQ ID NO:41. Any one of the splice variants described above can encode an amino acid sequence which contains at least one functional or structural characteristic of CGDD.

[0294] It will be appreciated by those skilled in the art that as a result of the degeneracy of the genetic code, a multitude of polynucleotide sequences encoding CGDD, some bearing minimal similarity to the polynucleotide sequences of any known and naturally occurring gene, may be produced. Thus, the invention contemplates each and every possible variation of polynucleotide sequence that could be made by selecting combinations based on possible codon choices. These combinations are made in accordance with the standard triplet genetic code as applied to the polynucleotide sequence of naturally occurring CGDD, and all such variations are to be considered as being specifically disclosed.

[0295] Although nucleotide sequences which encode CGDD and its variants are generally capable of hybridizing to the nucleotide sequence of the naturally occurring CGDD under appropriately selected conditions of stringency, it may be advantageous to produce nucleotide sequences encoding CGDD or its derivatives possessing a substantially different codon usage, e.g., inclusion of non-naturally occurring codons. Codons may be selected to increase the rate at which expression of the peptide occurs in a particular prokaryotic or eukaryotic host in accordance with the frequency with which particular codons are utilized by the host. Other reasons for substantially altering the nucleotide sequence encoding CGDD and its derivatives without altering the encoded amino acid sequences include the production of RNA transcripts having more desirable properties, such as a greater half-life, than transcripts produced from the naturally occurring sequence.

[0296] The invention also encompasses production of DNA sequences which encode CGDD and CGDD derivatives, or fragments thereof, entirely by synthetic chemistry. After production, the synthetic sequence maybe inserted into any of the many available expression vectors and cell systems using reagents well known in the art. Moreover, synthetic chemistry may be used to introduce mutations into a sequence encoding CGDD or any fragment thereof.

[0297] Also encompassed by the invention are polynucleotide sequences that are capable of hybridizing to the claimed polynucleotide sequences, and, in particular, to those shown in SEQ ID NO:22-42 and fragments thereof under various conditions of stringency. (See, e.g., Wahl, G. M. and S. L. Berger (1987) Methods Enzymol. 152:399-407; Kimmel, A. R. (1987) Methods Enzymol. 152:507-511.) Hybridization conditions, including annealing and wash conditions, are described in “Definitions.”

[0298] Methods for DNA sequencing are well known in the art and may be used to practice any of the embodiments of the invention. The methods may employ such enzymes as the Klenow fragment of DNA polymerase I, SEQUENASE (US Biochemical, Cleveland Ohio), Taq polymerase (Applied Biosystems), thermostable T7 polymerase (Amersham Pharmacia Biotech, Piscataway N.J.), or combinations of polymerases and proofreading exonucleases such as those found in the ELONGASE amplification system (Life Technologies, Gaithersburg Md.). Preferably, sequence preparation is automated with machines such as the MICROLAB 2200 liquid transfer system (Hamilton, Reno Nev.), PTC200 thermal cycler (MJ Research, Watertown Mass.) and ABI CATALYST 800 thermal cycler (Applied Biosystems). Sequencing is then carried out using either the ABI 373 or 377 DNA sequencing system (Applied Biosystems), the MEGABACE 1000 DNA sequencing system (Molecular Dynamics, Sunnyvale Calif.), or other systems known in the art. The resulting sequences are analyzed using a variety of algorithms which are well known in the art. (See, e.g., Ausubel, F. M. (1997) Short Protocols in Molecular Biology, John Wiley & Sons, New York N.Y., unit 7.7; Meyers, R. A. (1995) Molecular Biology and Biotechnology, Wiley VCH, New York N.Y., pp. 856-853.)

[0299] The nucleic acid sequences encoding CGDD may be extended utilizing a partial nucleotide sequence and employing various PCR-based methods known in the art to detect upstream sequences, such as promoters and regulatory elements. For example, one method which maybe employed, restriction-site PCR, uses universal and nested primers to amplify unknown sequence from genomic DNA within a cloning vector. (See, e.g., Sarkar, G. (1993) PCR Methods Applic. 2:318-322.) Another method, inverse PCR, uses primers that extend in divergent directions to amplify unknown sequence from a circularized template. The template is derived from restriction fragments comprising a known genomic locus and surrounding sequences. (See, e.g., Triglia, T. et al. (1988) Nucleic Acids Res. 16:8186.) A third method, capture PCR, involves PCR amplification of DNA fragments adjacent to known sequences in human and yeast artificial chromosome DNA. (See, e.g., Lagerstrom, M. et al. (1991) PCR Methods Applic. 1:111-119.) In this method, multiple restriction enzyme digestions and ligations may be used to insert an engineered double-stranded sequence into a region of unknown sequence before performing PCR. Other methods which may be used to retrieve unknown sequences are known in the art. (See, e.g., Parker, J. D. et al. (1991) Nucleic Acids Res. 19:3055-3060). Additionally, one may use PCR, nested primers, and PROMOTERFINDER libraries (Clontech, Palo Alto Calif.) to walk genomic DNA. This procedure avoids the need to screen libraries and is useful in finding intron/exon junctions. For all PCR-based methods, primers may be designed using commercially available software, such as OLIGO 4.06 primer analysis software (National Biosciences, Plymouth Minn.) or another appropriate program, to be about 22 to 30 nucleotides in length, to have a GC content of about 50% or more, and to anneal to the template at temperatures of about 68° C. to 72° C.

[0300] When screening for full length cDNAs, it is preferable to use libraries that have been size-selected to include larger cDNAs. In addition, random-primed libraries, which often include sequences containing the 5′ regions of genes, are preferable for situations in which an oligo d(T) library does not yield a full-length cDNA. Genomic libraries may be useful for extension of sequence into 5′ non-transcribed regulatory regions.

[0301] Capillary electrophoresis systems which are commercially available may be used to analyze the size or confirm the nucleotide sequence of sequencing or PCR products. In particular, capillary sequencing may employ flowable polymers for electrophoretic separation, four different nucleotide-specific, laser-stimulated fluorescent dyes, and a charge coupled device camera for detection of the emitted wavelengths. Output/light intensity may be converted to electrical signal using appropriate software (e.g., GENOTYPER and SEQUENCE NAVIGATOR, Applied Biosystems), and the entire process from loading of samples to computer analysis and electronic data display may be computer controlled. Capillary electrophoresis is especially preferable for sequencing small DNA fragments which may be present in limited amounts in a particular sample.

[0302] In another embodiment of the invention, polynucleotide sequences or fragments thereof which encode CGDD may be cloned in recombinant DNA molecules that direct expression of CGDD, or fragments or functional equivalents thereof, in appropriate host cells. Due to the inherent degeneracy of the genetic code, other DNA sequences which encode substantially the same or a functionally equivalent amino acid sequence may be produced and used to express CGDD.

[0303] The nucleotide sequences of the present invention can be engineered using methods generally known in the art in order to alter CGDD-encoding sequences for a variety of purposes including, but not limited to, modification of the cloning, processing, and/or expression of the gene product. DNA shuffling by random fragmentation and PCR reassembly of gene fragments and synthetic oligonucleotides may be used to engineer the nucleotide sequences. For example, oligonucleotide-mediated site-directed mutagenesis may be used to introduce mutations that create new restriction sites, alter glycosylation patterns, change codon preference, produce splice variants, and so forth.

[0304] The nucleotides of the present invention may be subjected to DNA shuffling techniques such as MOLECULARBREEDING (Maxygen Inc., Santa Clara Calif.; described in U.S. Pat. No. 5,837,458; Chang, C.-C. et al. (1999) Nat. Biotechnol. 17:793-797; Christians, F. C. et al. (1999) Nat. Biotechnol. 17:259-264; and Crameri, A. et al. (1996) Nat. Biotechnol. 14:315-319) to alter or improve the biological properties of CGDD, such as its biological or enzymatic activity or its ability to bind to other molecules or compounds. DNA shuffling is a process by which a library of gene variants is produced using PCR-mediated recombination of gene fragments. The library is then subjected to selection or screening procedures that identify those gene variants with the desired properties. These preferred variants may then be pooled and further subjected to recursive rounds of DNA shuffling and selection/screening. Thus, genetic diversity is created through “artificial” breeding and rapid molecular evolution. For example, fragments of a single gene containing random point mutations may be recombined, screened, and then reshuffled until the desired properties are optimized. Alternatively, fragments of a given gene may be recombined with fragments of homologous genes in the same gene family, either from the same or different species, thereby maximizing the genetic diversity of multiple naturally occurring genes in a directed and controllable manner.

[0305] In another embodiment, sequences encoding CGDD may be synthesized, in whole or in part, using chemical methods well known in the art. (See, e.g., Caruthers, M. H. et al. (1980) Nucleic Acids Symp. Ser. 7:215-223; and Horn, T. et al. (1980) Nucleic Acids Symp. Ser. 7:225-232.) Alternatively, CGDD itself or a fragment thereof may be synthesized using chemical methods. For example, peptide synthesis can be performed using various solution-phase or solid-phase techniques. (See, e.g., Creighton, T. (1984) Proteins, Structures and Molecular Properties, W H Freeman, New York N.Y., pp. 55-60; and Roberge, J. Y. et al. (1995) Science 269:202-204.) Automated synthesis maybe achieved using the ABI 431A peptide synthesizer (Applied Biosystems). Additionally, the amino acid sequence of CGDD, or any part thereof, may be altered during direct synthesis and/or combined with sequences from other proteins, or any part thereof, to produce a variant polypeptide or a polypeptide having a sequence of a naturally occurring polypeptide.

[0306] The peptide may be substantially purified by preparative high performance liquid chromatography. (See, e.g., Chiez, R. M. and F. Z. Regnier (1990) Methods Enzymol. 182:392-421.) The composition of the synthetic peptides may be confirmed by amino acid analysis or by sequencing. (See, e.g., Creighton, supra, pp. 28-53.)

[0307] In order to express a biologically active CGDD, the nucleotide sequences encoding CGDD or derivatives thereof may be inserted into an appropriate expression vector, i.e., a vector which contains the necessary elements for transcriptional and translational control of the inserted coding sequence in a suitable host. These elements include regulatory sequences, such as enhancers, constitutive and inducible promoters, and 5′ and 3′ untranslated regions in the vector and in polynucleotide sequences encoding CGDD. Such elements may vary in their strength and specificity. Specific initiation signals may also be used to achieve more efficient translation of sequences encoding CGDD. Such signals include the ATG initiation codon and adjacent sequences, e.g. the Kozak sequence. In cases where sequences encoding CGDD and its initiation codon and upstream regulatory sequences are inserted into the appropriate expression vector, no additional transcriptional or translational control signals may be needed. However, in cases where only coding sequence, or a fragment thereof, is inserted, exogenous translational control signals including an in-frame ATG initiation codon should be provided by the vector. Exogenous translational elements and initiation codons may be of various origins, both natural and synthetic. The efficiency of expression may be enhanced by the inclusion of enhancers appropriate for the particular host cell system used. (See, e.g., Scharf, D. et al. (1994) Results Probl. Cell Differ. 20:125-162.)

[0308] Methods which are well known to those skilled in the art may be used to construct expression vectors containing sequences encoding CGDD and appropriate transcriptional and translational control elements. These methods include in vitro recombinant DNA techniques, synthetic techniques, and in vivo genetic recombination. (See, e.g., Sambrook, J. et al. (1989) Molecular Cloning, A Laboratory Manual, Cold Spring Harbor Press, Plainview N.Y., ch. 4, 8, and 16-17; Ausubel, F. M. et al. (1995) Current Protocols in Molecular Biology, John Wiley & Sons, New York N.Y., ch. 9, 13, and 16.) A variety of expression vector/host systems may be utilized to contain and express sequences encoding CGDD. These include, but are not limited to, microorganisms such as bacteria transformed with recombinant bacteriophage, plasmid, or cosmid DNA expression vectors; yeast transformed with yeast expression vectors; insect cell systems infected with viral expression vectors (e.g., baculovirus); plant cell systems transformed with viral expression vectors (e.g., cauliflower mosaic virus, CaMV, or tobacco mosaic virus, TMV) or with bacterial expression vectors (e.g., Ti or pBR322 plasmids); or animal cell systems. (See, e.g., Sambrook, supra; Ausubel, supra; Van Heeke, G. and S. M. Schuster (1989) J. Biol. Chem. 264:5503-5509; Engelhard, E. K. et al. (1994) Proc. Natl. Acad. Sci. USA 91:3224-3227; Sandig, V. et al. (1996) Hum. Gene Ther. 7:1937-1945; Takamatsu, N. (1987) EMBO J. 6:307-311; The McGraw Hill Yearbook of Science and Technology (1992) McGraw Hill, New York N.Y., pp. 191-196; Logan, J. and T. Shenk (1984) Proc. Natl. Acad. Sci. USA 81:3655-3659; and Harrington, J. J. et al. (1997) Nat. Genet. 15:345-355.) Expression vectors derived from retroviruses, adenoviruses, or herpes or vaccinia viruses, or from various bacterial plasmids, may be used for delivery of nucleotide sequences to the targeted organ, tissue, or cell population. (See, e.g., Di Nicola, M. et al. (1998) Cancer Gen. Ther. 5(6):350-356; Yu, M. et al. (1993) Proc. Natl. Acad. Sci. USA 90(13):6340-6344; Buller, R. M. et al. (1985) Nature 317(6040):813-815; McGregor, D. P. et al. (1994) Mol. Immunol. 31(3):219-226; and Verma, I. M. and N. Somia (1997) Nature 389:239-242.) The invention is not limited by the host cell employed.

[0309] In bacterial systems, a number of cloning and expression vectors may be selected depending upon the use intended for polynucleotide sequences encoding CGDD. For example, routine cloning, subcloning, and propagation of polynucleotide sequences encoding CGDD can be achieved using a multifunctional E. coli vector such as PBLUESCRIPT (Stratagene, La Jolla Calif.) or PSPORT1 plasmid (Life Technologies). Ligation of sequences encoding CGDD into the vector's multiple cloning site disrupts the lacZ gene, allowing a colorimetric screening procedure for identification of transformed bacteria containing recombinant molecules. In addition, these vectors may be useful for in vitro transcription, dideoxy sequencing, single strand rescue with helper phage, and creation of nested deletions in the cloned sequence. (See, e.g., Van Heeke, G. and S. M. Schuster (1989) J. Biol. Chem. 264:5503-5509.) When large quantities of CGDD are needed, e.g. for the production of antibodies, vectors which direct high level expression of CGDD may be used. For example, vectors containing the strong, inducible SP6 or 17 bacteriophage promoter may be used.

[0310] Yeast expression systems may be used for production of CGDD. A number of vectors containing constitutive or inducible promoters, such as alpha factor, alcohol oxidase, and PGH promoters, may be used in the yeast Saccharomyces cerevisiae or Pichia pastoris. In addition, such vectors direct either the secretion or intracellular retention of expressed proteins and enable integration of foreign sequences into the host genome for stable propagation. (See, e.g., Ausubel, 1995, supra; Bitter, G. A. et al. (1987) Methods Enzymol. 153:516-544; and Scorer, C. A. et al. (1994) Bio/Technology 12:181-184.)

[0311] Plant systems may also be used for expression of CGDD. Transcription of sequences encoding CGDD may be driven by viral promoters, e.g., the 35S and 19S promoters of CaMV used alone or in combination with the omega leader sequence from TMV (Takamatsu, N. (1987) EMBO J. 6:307-311). Alternatively, plant promoters such as the small subunit of RUBISCO or heat shock promoters maybe used. (See, e.g., Coruzzi, G. et al. (1984) EMBO J. 3:1671-1680; Broglie, R. et al. (1984) Science 224:838-843; and Winter, J. et al. (1991) Results Probl. Cell Differ. 17:85-105.) These constructs can be introduced into plant cells by direct DNA transformation or pathogen-mediated transfection. (See, e.g., The McGraw Hill Yearbook of Science and Technology (1992) McGraw Hill, New York N.Y., pp. 191-196.)

[0312] In mammalian cells, a number of viral-based expression systems may be utilized. In cases where an adenovirus is used as an expression vector, sequences encoding CGDD may be ligated into an adenovirus transcription/translation complex consisting of the late promoter and tripartite leader sequence. Insertion in a non-essential E1 or E3 region of the viral genome may be used to obtain infective virus which expresses CGDD in host cells. (See, e.g., Logan, J. and T. Shenk (1984) Proc. Natl. Acad. Sci. USA 81:365.5-3659.) In addition, transcription enhancers, such as the Rous sarcoma virus (RSV) enhancer, may be used to increase expression in mammalian host cells. SV40 or EBV-based vectors may also be used for high-level protein expression.

[0313] Human artificial chromosomes (HACs) may also be employed to deliver larger fragments of DNA than can be contained in and expressed from a plasmid. HACs of about 6 kb to 10 Mb are constructed and delivered via conventional delivery methods (liposomes, polycationic amino polymers, or vesicles) for therapeutic purposes. (See, e.g., Harrington, J. J. et al. (1997) Nat. Genet. 15:345-355.)

[0314] For long term production of recombinant proteins in mammalian systems, stable expression of CGDD in cell lines is preferred. For example, sequences encoding CGDD can be transformed into cell lines using expression vectors which may contain viral origins of replication and/or endogenous expression elements and a selectable marker gene on the same or on a separate vector. Following the introduction of the vector, cells may be allowed to grow for about 1 to 2 days in enriched media before being switched to selective media. The purpose of the selectable marker is to confer resistance to a selective agent, and its presence allows growth and recovery of cells which successfully express the introduced sequences. Resistant clones of stably transformed cells may be propagated using tissue culture techniques appropriate to the cell type.

[0315] Any number of selection systems may be used to recover transformed cell lines. These include, but are not limited to, the herpes simplex virus thymidine kinase and adenine phosphoribosyltransferase genes, for use in tk⁻ and apr⁻ cells, respectively. (See, e.g., Wigler, M. et al. (1977) Cell 11:223-232; Lowy, I. et al. (1980) Cell 22:817-823.) Also, antimetabolite, antibiotic, or herbicide resistance can be used as the basis for selection. For example, dhfr confers resistance to methotrexate; neo confers resistance to the aminoglycosides neomycin and G-418; and als and pat confer resistance to chlorsulfuron and phosphinotricin acetyltransferase, respectively. (See, e.g., Wigler, M. et al. (1980) Proc. Natl. Acad. Sci. USA 77:3567-3570; Colbere-Garapin, F. et al. (1981) J. Mol. Biol. 150:1-14.) Additional selectable genes have been described, e.g., trpB and hisD, which alter cellular requirements for metabolites. (See, e.g., Hartman, S. C. and R. C. Mulligan (1988) Proc. Natl. Acad. Sci. USA 85:8047-8051.) Visible markers, e.g., anthocyanins, green fluorescent proteins (GFP; Clontech), β glucuronidase and its substrate β-glucuronide, or luciferase and its substrate luciferin may be used. These markers can be used not only to identify transformants, but also to quantify the amount of transient or stable protein expression attributable to a specific vector system. (See, e.g., Rhodes, C. A. (1995) Methods Mol. Biol. 55:121-131.)

[0316] Although the presence/absence of marker gene expression suggests that the gene of interest is also present, the presence and expression of the gene may need to be confirmed. For example, if the sequence encoding CGDD is inserted within a marker gene sequence, transformed cells containing sequences encoding CGDD can be identified by the absence of marker gene function. Alternatively, a marker gene can be placed in tandem with a sequence encoding CGDD under the control of a single promoter. Expression of the marker gene in response to induction or selection usually indicates expression of the tandem gene as well.

[0317] In general, host cells that contain the nucleic acid sequence encoding CGDD and that express CGDD may be identified by a variety of procedures known to those of skill in the art. These procedures include, but are not limited to, DNA-DNA or DNA-RNA hybridizations, PCR amplification, and protein bioassay or immunoassay techniques which include membrane, solution, or chip based technologies for the detection and/or quantification of nucleic acid or protein sequences.

[0318] Immunological methods for detecting and measuring the expression of CGDD using either specific polyclonal or monoclonal antibodies are known in the art. Examples of such techniques include enzyme-linked immunosorbent assays (ELISAs), radioimmunoassays (RIAs), and fluorescence activated cell sorting (FACS). A two-site, monoclonal-based immunoassay utilizing monoclonal antibodies reactive to two non-interfering epitopes on CGDD is preferred, but a competitive binding assay may be employed. These and other assays are well known in the art. (See, e.g., Hampton, R. et al. (1990) Serological Methods, a Laboratory Manual, APS Press, St. Paul Minn., Sect. IV; Coligan, J. E. et al. (1997) Current Protocols in Immunology, Greene Pub. Associates and Wiley-Interscience, New York N.Y.; and Pound, J. D. (1998) Immunochemical Protocols, Humana Press, Totowa N.J.)

[0319] A wide variety of labels and conjugation techniques are known by those skilled in the art and may be used in various nucleic acid and amino acid assays. Means for producing labeled hybridization or PCR probes for detecting sequences related to polynucleotides encoding CGDD include oligolabeling, nick translation, end-labeling, or PCR amplification using a labeled nucleotide. Alternatively, the sequences encoding CGDD, or any fragments thereof, may be cloned into a vector for the production of an mRNA probe. Such vectors are known in the art, are commercially available, and may be used to synthesize RNA probes in vitro by addition of an appropriate RNA polymerase such as T7, T3, or SP6 and labeled nucleotides. These procedures may be conducted using a variety of commercially available kits, such as those provided by Amersham Pharmacia Biotech, Promega (Madison Wis.), and US Biochemical. Suitable reporter molecules or labels which may be used for ease of detection include radionuclides, enzymes, fluorescent, chemiluminescent, or chromogenic agents, as well as substrates, cofactors, inhibitors, magnetic particles, and the like.

[0320] Host cells transformed with nucleotide sequences encoding CGDD may be cultured under conditions suitable for the expression and recovery of the protein from cell culture. The protein produced by a transformed cell may be secreted or retained intracellularly depending on the sequence and/or the vector used. As will be understood by those of skill in the art, expression vectors containing polynucleotides which encode CGDD may be designed to contain signal sequences which direct secretion of CGDD through a prokaryotic or eukaryotic cell membrane.

[0321] In addition, a host cell strain may be chosen for its ability to modulate expression of the inserted sequences or to process the expressed protein in the desired fashion. Such modifications of the polypeptide include, but are not limited to, acetylation, carboxylation, glycosylation, phosphorylation, lipidation, and acylation. Post-translational processing which cleaves a “prepro” or “pro” form of the protein may also be used to specify protein targeting, folding, and/or activity. Different host cells which have specific cellular machinery and characteristic mechanisms for post-translational activities (e.g., CHO, HeLa, MDCK, HEK293, and WI38) are available from the American Type Culture Collection (ATCC, Manassas Va.) and may be chosen to ensure the correct modification and processing of the foreign protein.

[0322] In another embodiment of the invention, natural, modified, or recombinant nucleic acid sequences encoding CGDD may be ligated to a heterologous sequence resulting in translation of a fusion protein in any of the aforementioned host systems. For example, a chimeric CGDD protein containing a heterologous moiety that can be recognized by a commercially available antibody may facilitate the screening of peptide libraries for inhibitors of CGDD activity. Heterologous protein and peptide moieties may also facilitate purification of fusion proteins using commercially available affinity matrices. Such moieties include, but are not limited to, glutathione S-transferase (GST), maltose binding protein (MBP), thioredoxin (Trx), calmodulin binding peptide (CBP), 6-His, FLAG, c-myc, and hemagglutinin (HA). GST, MBP, Trx, CBP, and 6-His enable purification of their cognate fusion proteins on immobilized glutathione, maltose, phenylarsine oxide, calmodulin, and metal-chelate resins, respectively. FLAG, c-myc, and hemagglutinin (HA) enable immunoaffinity purification of fusion proteins using commercially available monoclonal and polyclonal antibodies that specifically recognize these epitope tags. A fusion protein may also be engineered to contain a proteolytic cleavage site located between the CGDD encoding sequence and the heterologous protein sequence, so that CGDD may be cleaved away from the heterologous moiety following purification. Methods for fusion protein expression and purification are discussed in Ausubel (1995, supra, ch. 10). A variety of commercially available kits may also be used to facilitate expression and purification of fusion proteins.

[0323] In a further embodiment of the invention, synthesis of radiolabeled CGDD may be achieved in vitro using the TNT rabbit reticulocyte lysate or wheat germ extract system (Promega). These systems couple transcription and translation of protein-coding sequences operably associated with the T7, T3, or SP6 promoters. Translation takes place in the presence of a radiolabeled amino acid precursor, for example, ³⁵S-methionine.

[0324] CGDD of the present invention or fragments thereof may be used to screen for compounds that specifically bind to CGDD. At least one and up to a plurality of test compounds may be screened for specific binding to CGDD. Examples of test compounds include antibodies, oligonucleotides, proteins (e.g., receptors), or small molecules.

[0325] In one embodiment, the compound thus identified is closely related to the natural ligand of CGDD, e.g., a ligand or fragment thereof, a natural substrate, a structural or functional mimetic, or a natural binding partner. (See, e.g., Coligan, J. E. et al. (1991) Current Protocols in Immunology 1(2): Chapter 5.) Similarly, the compound can be closely related to the natural receptor to which CGDD binds, or to at least a fragment of the receptor, e.g., the ligand binding site. In either case, the compound can be rationally designed using known techniques. In one embodiment, screening for these compounds involves producing appropriate cells which express CGDD, either as a secreted protein or on the cell membrane. Preferred cells include cells from mammals, yeast, Drosophila, or E. coli. Cells expressing CGDD or cell membrane fractions which contain CGDD are then contacted with a test compound and binding, stimulation, or inhibition of activity of either CGDD or the compound is analyzed.

[0326] An assay may simply test binding of a test compound to the polypeptide, wherein binding is detected by a fluorophore, radioisotope, enzyme conjugate, or other detectable label. For example, the assay may comprise the steps of combining at least one test compound with CGDD, either in solution or affixed to a solid support, and detecting the binding of CGDD to the compound. Alternatively, the assay may detect or measure binding of a test compound in the presence of a labeled competitor. Additionally, the assay may be carried out using cell-free preparations, chemical libraries, or natural product mixtures, and the test compound(s) may be free in solution or affixed to a solid support.

[0327] CGDD of the present invention or fragments thereof may be used to screen for compounds that modulate the activity of CGDD. Such compounds may include agonists, antagonists, or partial or inverse agonists. In one embodiment, an assay is performed under conditions permissive for CGDD activity, wherein CGDD is combined with at least one test compound, and the activity of CGDD in the presence of a test compound is compared with the activity of CGDD in the absence of the test compound. A change in the activity of CGDD in the presence of the test compound is indicative of a compound that modulates the activity of CGDD. Alternatively, a test compound is combined with an in vitro or cell-free system comprising CGDD under conditions suitable for CGDD activity, and the assay is performed. In either of these assays, a test compound which modulates the activity of CGDD may do so indirectly and need not come in direct contact with the test compound. At least one and up to a plurality of test compounds may be screened.

[0328] In another embodiment, polynucleotides encoding CGDD or their mammalian homologs may be “knocked out” in an animal model system using homologous recombination in embryonic stem (ES) cells. Such techniques are well known in the art and are useful for the generation of animal models of human disease. (See, e.g., U.S. Pat. No. 5,175,383 and U.S. Pat. No. 5,767,337.) For example, mouse ES cells, such as the mouse 129/SvJ cell line, are derived from the early mouse embryo and grown in culture. The ES cells are transformed with a vector containing the gene of interest disrupted by a marker gene, e.g., the neomycin phosphotransferase gene (neo; Capecchi, M. R. (1989) Science 244:1288-1292). The vector integrates into the corresponding region of the host genome by homologous recombination. Alternatively, homologous recombination takes place using the Cre-loxP system to knockout a gene of interest in a tissue- or developmental stage-specific manner (Marth, J. D. (1996) Clin. Invest. 97:1999-2002; Wagner, K. U. et al. (1997) Nucleic Acids Res. 25:4323-4330). Transformed ES cells are identified and microinjected into mouse cell blastocysts such as those from the C57BL/6 mouse strain. The blastocysts are surgically transferred to pseudopregnant dams, and the resulting chimeric progeny are genotyped and bred to produce heterozygous or homozygous strains. Transgenic animals thus generated may be tested with potential therapeutic or toxic agents.

[0329] Polynucleotides encoding CGDD may also be manipulated in vitro in ES cells derived from human blastocysts. Human ES cells have the potential to differentiate into at least eight separate cell lineages including endoderm, mesoderm, and ectodermal cell types. These cell lineages differentiate into, for example, neural cells, hematopoietic lineages, and cardiomyocytes (Thomson, J. A. et al. (1998) Science 282:1145-1147).

[0330] Polynucleotides encoding CGDD can also be used to create “knockin” humanized animals (pigs) or transgenic animals (mice or rats) to model human disease. With knockin technology, a region of a polynucleotide encoding CGDD is injected into animal ES cells, and the injected sequence integrates into the animal cell genome. Transformed cells are injected into blastulae, and the blastulae are implanted as described above. Transgenic progeny or inbred lines are studied and treated with potential pharmaceutical agents to obtain information on treatment of a human disease. Alternatively, a mammal inbred to overexpress CGDD, e.g., by secreting CGDD in its milk, may also serve as a convenient source of that protein (Janne, J. et al. (1998) Biotechnol. Annu. Rev. 4:55-74).

[0331] Therapeutics

[0332] Chemical and structural similarity, e.g., in the context of sequences and motifs, exists between regions of CGDD and proteins associated with cell growth, differentiation, and death. In addition, examples of tissues expressing CGDD are breast cancer, PBMC cells, and brain cingulate tissue, and also can be found in Table 6. Therefore, CGDD appears to play a role in cell proliferative disorders including cancer, developmental disorders, neurological disorders, autoimmune/inflammatory disorders, reproductive disorders, and disorders of the placenta. In the treatment of disorders associated with increased CGDD expression or activity, it is desirable to decrease the expression or activity of CGDD. In the treatment of disorders associated with decreased CGDD expression or activity, it is desirable to increase the expression or activity of CGDD.

[0333] Therefore, in one embodiment, CGDD or a fragment or derivative thereof may be administered to a subject to treat or prevent a disorder associated with decreased expression or activity of CGDD. Examples of such disorders include, but are not limited to, a cell proliferative disorder such as actinic keratosis, arteriosclerosis, atherosclerosis, bursitis, cirrhosis, hepatitis, mixed connective tissue disease (MCTD), myelofibrosis, paroxysmal nocturnal hemoglobinuria, polycythemia vera, psoriasis, primary thrombocythemia, and cancers including adenocarcinoma, leukemia, lymphoma, melanoma, myeloma, sarcoma, teratocarcinoma, and, in particular, cancers of the adrenal gland, bladder, bone, bone marrow, brain, breast, cervix, gall bladder, ganglia, gastrointestinal tract, heart, kidney, liver, lung, muscle, ovary, pancreas, parathyroid, penis, prostate, salivary glands, skin, spleen, testis, thymus, thyroid, and uterus; a developmental disorder such as renal tubular acidosis, anemia, Cushing's syndrome, achondroplastic dwarfism, Duchenne and Becker muscular dystrophy, epilepsy, gonadal dysgenesis, WAGR syndrome (Wilms' tumor, aniridia, genitourinary abnormalities, and mental retardation), Smith-Magenis syndrome, myelodysplastic syndrome, hereditary mucoepithelial dysplasia, hereditary keratodermas, hereditary neuropathies such as Charcot-Marie-Tooth disease and neurofibromatosis, hypothyroidism, hydrocephalus, seizure disorders such as Syndenham's chorea and cerebral palsy, spina bifida, anencephaly, craniorachischisis, congenital glaucoma, cataract, and sensorineural hearing loss; a neurological disorder such as epilepsy, ischemic cerebrovascular disease, stroke, cerebral neoplasms, Alzheimer's disease, Pick's disease, Huntington's disease, dementia, Parkinson's disease and other extrapyramidal disorders, amyotrophic lateral sclerosis and other motor neuron disorders, progressive neural muscular atrophy, retinitis pigmentosa, hereditary ataxias, multiple sclerosis and other demyelinating diseases, bacterial and viral meningitis, brain abscess, subdural empyema, epidural abscess, suppurative intracranial thrombophlebitis, myelitis and radiculitis, viral central nervous system disease, prion diseases including kuru, Creutzfeldt-Jakob disease, and Gerstmann-Straussler-Scheinker syndrome, fatal familial insomnia, nutritional and metabolic diseases of the nervous system, neurofibromatosis, tuberous sclerosis, cerebelloretinal hemangioblastomatosis, encephalotrigeminal syndrome, mental retardation and other developmental disorders of the central nervous system including Down syndrome, cerebral palsy, neuroskeletal disorders, autonomic nervous system disorders, cranial nerve disorders, spinal cord diseases, muscular dystrophy and other neuromuscular disorders, peripheral nervous system disorders, dermatomyositis and polymyositis, inherited, metabolic, endocrine, and toxic myopathies, myasthenia gravis, periodic paralysis, mental disorders including mood, anxiety, and schizophrenic disorders, seasonal affective disorder (SAD), akathesia, amnesia, catatonia, diabetic neuropathy, tardive dyskinesia, dystonias, paranoid psychoses, postherpetic neuralgia, Tourette's disorder, progressive supranuclear palsy, corticobasal degeneration, and familial frontotemporal dementia; an autoimmune/inflammatory disorder such as acquired immunodeficiency syndrome (AIDS), Addison's disease, adult respiratory distress syndrome, allergies, ankylosing spondylitis, amyloidosis, anemia, asthma, atherosclerosis, autoimmune hemolytic anemia, autoimmune thyroiditis, autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy (APECED), bronchitis, cholecystitis, contact dermatitis, Crohn's disease, atopic dermatitis, dermatomyositis, diabetes mellitus, emphysema, episodic lymphopenia with lymphocytotoxins, erythroblastosis fetalis, erythema nodosum, atrophic gastritis, glomerulonephritis, Goodpasture's syndrome, gout, Graves' disease, Hashimoto's thyroiditis, hypereosinophilia, irritable bowel syndrome, multiple sclerosis, myasthenia gravis, myocardial or pericardial inflammation, osteoarthritis, osteoporosis, pancreatitis, polymyositis, psoriasis, Reiter's syndrome, rheumatoid arthritis, scleroderma, Sjögren's syndrome, systemic anaphylaxis, systemic lupus erythematosus, systemic sclerosis, thrombocytopenic purpura, ulcerative colitis, uveitis, Werner syndrome, complications of cancer, hemodialysis, and extracorporeal circulation, viral, bacterial, fungal, parasitic, protozoal, and helminthic infections, and trauma; a reproductive disorder such as a disorder of prolactin production, infertility, including tubal disease, ovulatory defects, endometriosis, a disruption of the estrous cycle, a disruption of the menstrual cycle, polycystic ovary syndrome, ovarian hyperstimulation syndrome, an endometrial or ovarian tumor, a uterine fibroid, autoimmune disorders, ectopic pregnancy, teratogenesis; cancer of the breast, fibrocystic breast disease, galactorrhea; a disruption of spermatogenesis, abnormal sperm physiology, cancer of the testis, cancer of the prostate, benign prostatic hyperplasia, prostatitis, Peyronie's disease, impotence, carcinoma of the male breast, gynecomastia, hypergonadotropic and hypogonadotropic hypogonadism, pseudohermaphroditism, azoospermia, premature ovarian failure, acrosin deficiency, delayed puperty, retrograde ejaculation and anejaculation, haemangioblastomas, cystsphaeochromocytomas, paraganglioma, cystadenomas of the epididymis, and endolymphatic sac tumors; and a disorder of the placenta such as preeclampsia, choriocarcinoma, abruptio placentae, placenta previa, placental or maternal floor infarction, placenta accreta, increate, and percreta, extrachorial placentas, chorangioma, chorangiosis, chronic villitis, placental villous endema, widespread fibrosis of the terminal villi, intervillous thrombi, hemorraghic endovasculitis, erythroblastosis fetalis, and nonimmune fetal hydrops.

[0334] In another embodiment, a vector capable of expressing CGDD or a fragment or derivative thereof may be administered to a subject to treat or prevent a disorder associated with decreased expression or activity of CGDD including, but not limited to, those described above.

[0335] In a further embodiment, a composition comprising a substantially purified CGDD in conjunction with a suitable pharmaceutical carrier may be administered to a subject to treat or prevent a disorder associated with decreased expression or activity of CGDD including, but not limited to, those provided above.

[0336] In still another embodiment, an agonist which modulates the activity of CGDD may be administered to a subject to treat or prevent a disorder associated with decreased expression or activity of CGDD including, but not limited to, those listed above.

[0337] In a further embodiment, an antagonist of CGDD may be administered to a subject to treat or prevent a disorder associated with increased expression or activity of CGDD. Examples of such disorders include, but are not limited to, those cell proliferative disorders including cancer, developmental disorders, neurological disorders, autoimmune/inflammatory disorders, reproductive disorders, and disorders of the placenta described above. In one aspect, an antibody which specifically binds CGDD may be used directly as an antagonist or indirectly as a targeting or delivery mechanism for bringing a pharmaceutical agent to cells or tissues which express CGDD.

[0338] In an additional embodiment, a vector expressing the complement of the polynucleotide encoding CGDD may be administered to a subject to treat or prevent a disorder associated with increased expression or activity of CGDD including, but not limited to, those described above.

[0339] In other embodiments, any of the proteins, antagonists, antibodies, agonists, complementary sequences, or vectors of the invention may be administered in combination with other appropriate therapeutic agents. Selection of the appropriate agents for use in combination therapy may be made by one of ordinary skill in the art, according to conventional pharmaceutical principles. The combination of therapeutic agents may act synergistically to effect the treatment or prevention of the various disorders described above. Using this approach, one may be able to achieve therapeutic efficacy with lower dosages of each agent, thus reducing the potential for adverse side effects.

[0340] An antagonist of CGDD maybe produced using methods which are generally known in the art. In particular, purified CGDD may be used to produce antibodies or to screen libraries of pharmaceutical agents to identify those which specifically bind CGDD. Antibodies to CGDD may also be generated using methods that are well known in the art. Such antibodies may include, but are not limited to, polyclonal, monoclonal, chimeric, and single chain antibodies, Fab fragments, and fragments produced by a Fab expression library. Neutralizing antibodies (i.e., those which inhibit dimer formation) are generally preferred for therapeutic use. Single chain antibodies (e.g., from camels or llamas) may be potent enzyme inhibitors and may have advantages in the design of peptide mimetics, and in the development of immuno-adsorbents and biosensors (Muyldermans, S. (2001) J. Biotechnol. 74:277-302).

[0341] For the production of antibodies, various hosts including goats, rabbits, rats, mice, camels, dromedaries, llamas, humans, and others may be immunized by injection with CGDD or with any fragment or oligopeptide thereof which has immunogenic properties. Depending on the host species, various adjuvants may be used to increase immunological response. Such adjuvants include, but are not limited to, Freund's, mineral gels such as aluminum hydroxide, and surface active substances such as lysolecithin, pluronic polyols, polyanions, peptides, oil emulsions, KLH, and dinitrophenol. Among adjuvants used in humans, BCG (bacilli Calmette-Guerin) and Corynebacterium parvum are especially preferable.

[0342] It is preferred that the oligopeptides, peptides, or fragments used to induce antibodies to CGDD have an amino acid sequence consisting of at least about 5 amino acids, and generally will consist of at least about 10 amino acids. It is also preferable that these oligopeptides, peptides, or fragments are identical to a portion of the amino acid sequence of the natural protein. Short stretches of CGDD amino acids may be fused with those of another protein, such as KLH, and antibodies to the chimeric molecule may be produced.

[0343] Monoclonal antibodies to CGDD may be prepared using any technique which provides for the production of antibody molecules by continuous cell lines in culture. These include, but are not limited to, the hybridoma technique, the human B-cell hybridoma technique, and the EBV-hybridoma technique. (See, e.g., Kohler, G. et al. (1975) Nature 256:495-497; Kozbor, D. et al. (1985) J. Immunol. Methods 81:31-42; Cote, R. J. et al. (1983) Proc. Natl. Acad. Sci. USA 80:2026-2030; and Cole, S. P. et al. (1984) Mol. Cell Biol. 62:109-120.)

[0344] In addition, techniques developed for the production of “ chimeric antibodies,” such as the splicing of mouse antibody genes to human antibody genes to obtain a molecule with appropriate antigen specificity and biological activity, can be used. (See, e.g., Morrison, S. L. et al. (1984) Proc. Natl. Acad. Sci. USA 81:6851-6855; Neuberger, M. S. et al. (1984) Nature 312:604-608; and Takeda, S. et al. (1985) Nature 314:452-454.) Alternatively, techniques described for the production of single chain antibodies may be adapted, using methods known in the art, to produce CGDD-specific single chain antibodies. Antibodies with related specificity, but of distinct idiotypic composition, may be generated by chain shuffling from random combinatorial immunoglobulin libraries. (See, e.g., Burton, D. R. (1991) Proc. Natl. Acad. Sci. USA 88:10134-10137.)

[0345] Antibodies may also be produced by inducing in vivo production in the lymphocyte population or by screening immunoglobulin libraries or panels of highly specific binding reagents as disclosed in the literature. (See, e.g., Orlandi, R. et al. (1989) Proc. Natl. Acad. Sci. USA 86:3833-3837; Winter, G. et al. (1991) Nature 349:293-299.)

[0346] Antibody fragments which contain specific binding sites for CGDD may also be generated. For example, such fragments include, but are not limited to, F(ab′)₂ fragments produced by pepsin digestion of the antibody molecule and Fab fragments generated by reducing the disulfide bridges of the F(ab′)₂ fragments. Alternatively, Fab expression libraries may be constructed to allow rapid and easy identification of monoclonal Fab fragments with the desired specificity. (See, e.g., Huse, W. D. et al. (1989) Science 246:1275-1281.)

[0347] Various immunoassays may be used for screening to identify antibodies having the desired specificity. Numerous protocols for competitive binding or immunoradiometric assays using either polyclonal or monoclonal antibodies with established specificities are well known in the art. Such immunoassays typically involve the measurement of complex formation between CGDD and its specific antibody. A two-site, monoclonal-based immunoassay utilizing monoclonal antibodies reactive to two non-interfering CGDD epitopes is generally used, but a competitive binding assay may also be employed (Pound, supra).

[0348] Various methods such as Scatchard analysis in conjunction with radioimmunoassay techniques may be used to assess the affinity of antibodies for CGDD. Affinity is expressed as an association constant, K_(a), which is defined as the molar concentration of CGDD-antibody complex divided by the molar concentrations of free antigen and free antibody under equilibrium conditions. The K_(a) determined for a preparation of polyclonal antibodies, which are heterogeneous in their affinities for multiple CGDD epitopes, represents the average affinity, or avidity, of the antibodies for CGDD. The K_(a) determined for a preparation of monoclonal antibodies, which are monospecific for a particular CGDD epitope, represents a true measure of affinity. High-affinity antibody preparations with K_(a) ranging from about 10⁹ to 10¹² L/mole are preferred for use in immunoassays in which the CGDD-antibody complex must withstand rigorous manipulations. Low-affinity antibody preparations with K_(a) ranging from about 10⁶ to 10⁷ L/mole are preferred for use in immunopurification and similar procedures which ultimately require dissociation of CGDD, preferably in active form, from the antibody (Catty, D. (1988) Antibodies, Volume I: A Practical Approach, IRL Press, Washington D.C.; Liddell, J. E. and A. Cryer (1991) A Practical Guide to Monoclonal Antibodies, John Wiley & Sons, New York N.Y.).

[0349] The titer and avidity of polyclonal antibody preparations may be further evaluated to determine the quality and suitability of such preparations for certain downstream applications. For example, a polyclonal antibody preparation containing at least 1-2 mg specific antibody/ml, preferably 5-10 mg specific antibody/ml, is generally employed in procedures requiring precipitation of CGDD-antibody complexes. Procedures for evaluating antibody specificity, titer, and avidity, and guidelines for antibody quality and usage in various applications, are generally available. (See, e.g., Catty, supra, and Coligan et al. supra.)

[0350] In another embodiment of the invention, the polynucleotides encoding CGDD, or any fragment or complement thereof, may be used for therapeutic purposes. In one aspect, modifications of gene expression can be achieved by designing complementary sequences or antisense molecules (DNA, RNA, PNA, or modified oligonucleotides) to the coding or regulatory regions of the gene encoding CGDD. Such technology is well known in the art, and antisense oligonucleotides or larger fragments can be designed from various locations along the coding or control regions of sequences encoding CGDD. (See, e.g., Agrawal, S., ed. (1996) Antisense Therapeutics, Humana Press Inc., Totawa N.J.)

[0351] In therapeutic use, any gene delivery system suitable for introduction of the antisense sequences into appropriate target cells can be used. Antisense sequences can be delivered intracellularly in the form of an expression plasmid which, upon transcription, produces a sequence complementary to at least a portion of the cellular sequence encoding the target protein. (See, e.g., Slater, J. E. et al. (1998) J. Allergy Clin. Immunol. 102(3):469-475; and Scanlon, K. J. et al. (1995) 9(13):1288-1296.) Antisense sequences can also be introduced intracellularly through the use of viral vectors, such as retrovirus and adeno-associated virus vectors. (See, e.g., Miller, A. D. (1990) Blood 76:271; Ausubel, supra; Uckert, W. and W. Walther (1994) Pharmacol. Ther. 63(3):323-347.) Other gene delivery mechanisms include liposome-derived systems, artificial viral envelopes, and other systems known in the art. (See, e.g., Rossi, J. J. (1995) Br. Med. Bull. 51(1):217-225; Boado, R. J. et al. (1998) J. Pharm. Sci. 87(11):1308-1315; and Morris, M. C. et al. (1997) Nucleic Acids Res. 25(14):2730-2736.)

[0352] In another embodiment of the invention, polynucleotides encoding CGDD may be used for somatic or germline gene therapy. Gene therapy may be performed to (i) correct a genetic deficiency (e.g., in the cases of severe combined immunodeficiency (SCID)-X1 disease characterized by X-linked inheritance (Cavazzana-Calvo, M. et al. (2000) Science 288:669-672), severe combined immunodeficiency syndrome associated with an inherited adenosine deaminase (ADA) deficiency (Blaese, R. M. et al. (1995) Science 270:475-480; Bordignon, C. et al. (1995) Science 270:470-475), cystic fibrosis (Zabner, J. et al. (1993) Cell 75:207-216; Crystal, R. G. et al. (1995) Hum. Gene Therapy 6:643-666; Crystal, R. G. et al. (1995) Hum. Gene Therapy 6:667-703), thalassamias, familial hypercholesterolemia, and hemophilia resulting from Factor VIII or Factor IX deficiencies (Crystal, R. G. (1995) Science 270:404-410; Verma, I. M. and N. Somia (1997) Nature 389:239-242)), (ii) express a conditionally lethal gene product (e.g., in the case of cancers which result from unregulated cell proliferation), or (iii) express a protein which affords protection against intracellular parasites (e.g., against human retroviruses, such as human immunodeficiency virus (HIV) (Baltimore, D. (1988) Nature 335:395-396; Poeschla, E. et al. (1996) Proc. Natl. Acad. Sci. USA 93:11395-11399), hepatitis B or C virus (HBV, HCV); fungal parasites, such as Candida albicans and Paracoccidioides brasiliensis; and protozoan parasites such as Plasmodium falciparum and Trypanosoma cruzi). In the case where a genetic deficiency in CGDD expression or regulation causes disease, the expression of CGDD from an appropriate population of transduced cells may alleviate the clinical manifestations caused by the genetic deficiency.

[0353] In a further embodiment of the invention, diseases or disorders caused by deficiencies in CGDD are treated by constructing mammalian expression vectors encoding CGDD and introducing these vectors by mechanical means into CGDD-deficient cells. Mechanical transfer technologies for use with cells in vivo or ex vitro include (i) direct DNA microinjection into individual cells, (ii) ballistic gold particle delivery, (iii) liposome-mediated transfection, (iv) receptor-mediated gene transfer, and (v) the use of DNA transposons (Morgan, R. A. and W. F. Anderson (1993) Annu. Rev. Biochem. 62:191-217; Ivics, Z. (1997) Cell 91:501-510; Boulay, J-L. and H. Récipon (1998) Curr. Opin. Biotechnol. 9:445-450).

[0354] Expression vectors that may be effective for the expression of CGDD include, but are not limited to, the PCDNA 3.1, EPITAG, PRCCMV2, PREP, PVAX, PCR2-TOPOTA vectors (Invitrogen, Carlsbad Calif.), PCMV-SCRIPT, PCMV-TAG, PEGSH/PERV (Stratagene, La Jolla Calif.), and PTET-OFF, PTET-ON, PTRE2, PTRE2-LUC, PTK-HYG (Clontech, Palo Alto Calif.). CGDD may be expressed using (i) a constitutively active promoter, (e.g., from cytomegalovirus (CMV), Rous sarcoma virus (RSV), SV40 virus, thymidine kinase (TK), or β-actin genes), (ii) an inducible promoter (e.g., the tetracycline-regulated promoter (Gossen, M. and H. Bujard (1992) Proc. Natl. Acad. Sci. USA 89:5547-5551; Gossen, M. et al. (1995) Science 268:1766-1769; Rossi, F. M. V. and H. M. Blau (1998) Curr. Opin. Biotechnol. 9:451-456), commercially available in the T-REX plasmid (Invitrogen)); the ecdysone-inducible promoter (available in the plasmids PVGRXR and PIND; Invitrogen); the FK506/rapamycin inducible promoter; or the RU486/mifepristone inducible promoter (Rossi, F. M. V. and H. M. Blau, supra)), or (iii) a tissue-specific promoter or the native promoter of the endogenous gene encoding CGDD from a normal individual.

[0355] Commercially available liposome transformation kits (e.g., the PERFECT LIPID TRANSFECTION KIT, available from Invitrogen) allow one with ordinary skill in the art to deliver polynucleotides to target cells in culture and require minimal effort to optimize experimental parameters. In the alternative, transformation is performed using the calcium phosphate method (Graham, F. L. and A. J. Eb (1973) Virology 52:456-467), or by electroporation (Neumann, E. et al. (1982) EMBO J. 1:841-845). The introduction of DNA to primary cells requires modification of these standardized mammalian transfection protocols.

[0356] In another embodiment of the invention, diseases or disorders caused by genetic defects with respect to CGDD expression are treated by constructing a retrovirus vector consisting of (i) the polynucleotide encoding CGDD under the control of an independent promoter or the retrovirus long terminal repeat (LTR) promoter, (ii) appropriate RNA packaging signals, and (iii) a Rev-responsive element (RRE) along with additional retrovirus cis-acting RNA sequences and coding sequences required for efficient vector propagation. Retrovirus vectors (e.g., PFB and PFBNEO) are commercially available (Stratagene) and are based on published data (Riviere, I. et al. (1995) Proc. Natl. Acad. Sci. USA 92:6733-6737), incorporated by reference herein. The vector is propagated in an appropriate vector producing cell line (VPCL) that expresses an envelope gene with a tropism for receptors on the target cells or a promiscuous envelope protein such as VSVg (Armentano, D. et al. (1987) J. Virol. 61:1647-1650; Bender, M. A. et al. (1987) J. Virol. 61:1639-1646; Adam, M. A. and A. D. Miller (1988) J. Virol. 62:3802-3806; Dull, T. et al. (1998) J. Virol. 72:8463-8471; Zufferey, R. et al. (1998) J. Virol. 72:9873-9880). U.S. Pat. No. 5,910,434 to Rigg (“Method for obtaining retrovirus packaging cell lines producing high transducing efficiency retroviral supernatant”) discloses a method for obtaining retrovirus packaging cell lines and is hereby incorporated by reference. Propagation of retrovirus vectors, transduction of a population of cells (e.g., CD4⁺ T-cells), and the return of transduced cells to a patient are procedures well known to persons skilled in the art of gene therapy and have been well documented (Ranga, U. et al. (1997) J. Virol. 71:7020-7029; Bauer, G. et al. (1997) Blood 89:2259-2267; Bonyhadi, M. L. (1997) J. Virol. 71:4707-4716; Ranga, U. et al. (1998) Proc. Natl. Acad. Sci. USA 95:1201-1206; Su, L. (1997) Blood 89-2283-2290).

[0357] In the alternative, an adenovirus-based gene therapy delivery system is used to deliver polynucleotides encoding CGDD to cells which have one or more genetic abnormalities with respect to the expression of CGDD. The construction and packaging of adenovirus-based vectors are well known to those with ordinary skill in the art. Replication defective adenovirus vectors have proven to be versatile for importing genes encoding immunoregulatory proteins into intact islets in the pancreas (Csete, M. E. et al. (1995) Transplantation 27:263-268). Potentially useful adenoviral vectors are described in U.S. Pat. No. 5,707,618 to Armentano (“Adenovirus vectors for gene therapy”), hereby incorporated by reference. For adenoviral vectors, see also Antinozzi, P. A. et al. (1999) Annu. Rev. Nutr. 19:511-544 and Verma, I. M. and N. Somia (1997) Nature 18:389:239-242, both incorporated by reference herein.

[0358] In another alternative, a herpes-based, gene therapy delivery system is used to deliver polynucleotides encoding CGDD to target cells which have one or more genetic abnormalities with respect to the expression of CGDD. The use of herpes simplex virus (HSV)-based vectors may be especially valuable for introducing CGDD to cells of the central nervous system, for which HSV has a tropism. The construction and packaging of herpes-based vectors are well known to those with ordinary skill in the art. A replication-competent herpes simplex virus (HSV) type 1-based vector has been used to deliver a reporter gene to the eyes of primates (Liu, X. et al. (1999) Exp. Eye Res. 169:385-395). The construction of a HSV-1 virus vector has also been disclosed in detail in U.S. Pat. No. 5,804,413 to DeLuca (“Herpes simplex virus strains for gene transfer”), which is hereby incorporated by reference. U.S. Pat. No. 5,804,413 teaches the use of recombinant HSV d92 which consists of a genome containing at least one exogenous gene to be transferred to a cell under the control of the appropriate promoter for purposes including human gene therapy. Also taught by this patent are the construction and use of recombinant HSV strains deleted for ICP4, ICP27 and ICP22. For HSV vectors, see also Goins, W. F. et al. (1999) J. Virol. 73:519-532 and Xu, H. et al. (1994) Dev. Biol. 163:152-161, hereby incorporated by reference. The manipulation of cloned herpesvirus sequences, the generation of recombinant virus following the transfection of multiple plasmids containing different segments of the large herpesvirus genomes, the growth and propagation of herpesvirus, and the infection of cells with herpesvirus are techniques well known to those of ordinary skill in the art.

[0359] In another alternative, an alphavirus (positive, single-stranded RNA virus) vector is used to deliver polynucleotides encoding CGDD to target cells. The biology of the prototypic alphavirus, Semliki Forest Virus (SFV), has been studied extensively and gene transfer vectors have been based on the SFV genome (Garoff, H. and K.-J. Li (1998) Curr. Opin. Biotechnol. 9:464-469). During alphavirus RNA replication, a subgenomic RNA is generated that normally encodes the viral capsid proteins. This subgenomic RNA replicates to higher levels than the full length genomic RNA, resulting in the overproduction of capsid proteins relative to the viral proteins with enzymatic activity (e.g., protease and polymerase). Similarly, inserting the coding sequence for CGDD into the alphavirus genome in place of the capsid-coding region results in the production of a large number of CGDD-coding RNAs and the synthesis of high levels of CGDD in vector transduced cells. While alphavirus infection is typically associated with cell lysis within a few days, the ability to establish a persistent infection in hamster normal kidney cells (BHK-21) with a variant of Sindbis virus (SIN) indicates that the lytic replication of alphaviruses can be altered to suit the needs of the gene therapy application (Dryga, S. A. et al. (1997) Virology 228:74-83). The wide host range of alphaviruses will allow the introduction of CGDD into a variety of cell types. The specific transduction of a subset of cells in a population may require the sorting of cells prior to transduction. The methods of manipulating infectious cDNA clones of alphaviruses, performing alphavirus cDNA and RNA transfections, and performing alphavirus infections, are well known to those with ordinary skill in the art.

[0360] Oligonucleotides derived from the transcription initiation site, e.g., between about positions −10 and +10 from the start site, may also be employed to inhibit gene expression. Similarly, inhibition can be achieved using triple helix base-pairing methodology. Triple helix pairing is useful because it causes inhibition of the ability of the double helix to open sufficiently for the binding of polymerases, transcription factors, or regulatory molecules. Recent therapeutic advances using triplex DNA have been described in the literature. (See, e.g., Gee, J. E. et al. (1994) in Huber, B. E. and B. I. Carr, Molecular and Immunologic Approaches, Futura Publishing, Mt. Kisco N.Y., pp. 163-177.) A complementary sequence or antisense molecule may also be designed to block translation of mRNA by preventing the transcript from binding to ribosomes.

[0361] Ribozymes, enzymatic RNA molecules, may also be used to catalyze the specific cleavage of RNA. The mechanism of ribozyme action involves sequence-specific hybridization of the ribozyme molecule to complementary target RNA, followed by endonucleolytic cleavage. For example, engineered hammerhead motif ribozyme molecules may specifically and efficiently catalyze endonucleolytic cleavage of sequences encoding CGDD.

[0362] Specific ribozyme cleavage sites within any potential RNA target are initially identified by scanning the target molecule for ribozyme cleavage sites, including the following sequences: GUA, GUU, and GUC. Once identified, short RNA sequences of between 15 and 20 ribonucleotides, corresponding to the region of the target gene containing the cleavage site, may be evaluated for secondary structural features which may render the oligonucleotide inoperable. The suitability of candidate targets may also be evaluated by testing accessibility to hybridization with complementary oligonucleotides using ribonuclease protection assays.

[0363] Complementary ribonucleic acid molecules and ribozymes of the invention may be prepared by any method known in the art for the synthesis of nucleic acid molecules. These include techniques for chemically synthesizing oligonucleotides such as solid phase phosphoramidite chemical synthesis. Alternatively, RNA molecules may be generated by in vitro and in vivo transcription of DNA sequences encoding CGDD. Such DNA sequences may be incorporated into a wide variety of vectors with suitable RNA polymerase promoters such as T7 or SP6. Alternatively, these cDNA constructs that synthesize complementary RNA, constitutively or inducibly, can be introduced into cell lines, cells, or tissues.

[0364] RNA molecules may be modified to increase intracellular stability and half-life. Possible modifications include, but are not limited to, the addition of flanking sequences at the 5′ and/or 3′ ends of the molecule, or the use of phosphorothioate or 2′O-methyl rather than phosphodiesterase linkages within the backbone of the molecule. This concept is inherent in the production of PNAs and can be extended in all of these molecules by the inclusion of nontraditional bases such as inosine, queosine, and wybutosine, as well as acetyl-, methyl-, thio-, and similarly modified forms of adenine, cytidine, guanine, thymine, and uridine which are not as easily recognized by endogenous endonucleases.

[0365] An additional embodiment of the invention encompasses a method for screening for a compound which is effective in altering expression of a polynucleotide encoding CGDD. Compounds which may be effective in altering expression of a specific polynucleotide may include, but are not limited to, oligonucleotides, antisense oligonucleotides, triple helix-forming oligonucleotides, transcription factors and other polypeptide transcriptional regulators, and non-macromolecular chemical entities which are capable of interacting with specific polynucleotide sequences. Effective compounds may alter polynucleotide expression by acting as either inhibitors or promoters of polynucleotide expression. Thus, in the treatment of disorders associated with increased CGDD expression or activity, a compound which specifically inhibits expression of the polynucleotide encoding CGDD may be therapeutically useful, and in the treatment of disorders associated with decreased CGDD expression or activity, a compound which specifically promotes expression of the polynucleotide encoding CGDD may be therapeutically useful.

[0366] At least one, and up to a plurality, of test compounds may be screened for effectiveness in altering expression of a specific polynucleotide. A test compound may be obtained by any method commonly known in the art, including chemical modification of a compound known to be effective in altering polynucleotide expression; selection from an existing, commercially-available or proprietary library of naturally-occurring or non-natural chemical compounds; rational design of a compound based on chemical and/or structural properties of the target polynucleotide; and selection from a library of chemical compounds created combinatorially or randomly. A sample comprising a polynucleotide encoding CGDD is exposed to at least one test compound thus obtained. The sample may comprise, for example, an intact or permeabilized cell, or an in vitro cell-free or reconstituted biochemical system. Alterations in the expression of a polynucleotide encoding CGDD are assayed by any method commonly known in the art. Typically, the expression of a specific nucleotide is detected by hybridization with a probe having a nucleotide sequence complementary to the sequence of the polynucleotide encoding CGDD. The amount of hybridization may be quantified, thus forming the basis for a comparison of the expression of the polynucleotide both with and without exposure to one or more test compounds. Detection of a change in the expression of a polynucleotide exposed to a test compound indicates that the test compound is effective in altering the expression of the polynucleotide. A screen for a compound effective in altering expression of a specific polynucleotide can be carried out, for example, using a Schizosaccharomyces pombe gene expression system (Atkins, D. et al. (1999) U.S. Pat. No. 5,932,435; Arndt, G. M. et al. (2000) Nucleic Acids Res. 28:E15) or a human cell line such as HeLa cell (Clarke, M. L. et al. (2000) Biochem. Biophys. Res. Commun. 268:8-13). A particular embodiment of the present invention involves screening a combinatorial library of oligonucleotides (such as deoxyribonucleotides, ribonucleotides, peptide nucleic acids, and modified oligonucleotides) for antisense activity against a specific polynucleotide sequence (Bruice, T. W. et al. (1997) U.S. Pat. No. 5,686,242; Bruice, T. W. et al. (2000) U.S. Pat. No. 6,022,691).

[0367] Many methods for introducing vectors into cells or tissues are available and equally suitable for use in vivo, in vitro, and ex vivo. For ex vivo therapy, vectors may be introduced into stem cells taken from the patient and clonally propagated for autologous transplant back into that same patient. Delivery by transfection, by liposome injections, or by polycationic amino polymers may be achieved using methods which are well known in the art. (See, e.g., Goldman, C. K. et al. (1997) Nat. Biotechnol. 15:462-466.)

[0368] Any of the therapeutic methods described above may be applied to any subject in need of such therapy, including, for example, mammals such as humans, dogs, cats, cows, horses, rabbits, and monkeys.

[0369] An additional embodiment of the invention relates to the administration of a composition which generally comprises an active ingredient formulated with a pharmaceutically acceptable excipient. Excipients may include, for example, sugars, starches, celluloses, gums, and proteins. Various formulations are commonly known and are thoroughly discussed in the latest edition of Remington's Pharmaceutical Sciences (Maack Publishing, Easton Pa.). Such compositions may consist of CGDD, antibodies to CGDD, and mimetics, agonists, antagonists, or inhibitors of CGDD.

[0370] The compositions utilized in this invention may be administered by any number of routes including, but not limited to, oral, intravenous, intramuscular, intra-arterial, intramedullary, intrathecal, intraventricular, pulmonary, transdermal, subcutaneous, intraperitoneal, intranasal, enteral, topical, sublingual, or rectal means.

[0371] Compositions for pulmonary administration may be prepared in liquid or dry powder form. These compositions are generally aerosolized immediately prior to inhalation by the patient. In the case of small molecules (e.g. traditional low molecular weight organic drugs), aerosol delivery of fast-acting formulations is well-known in the art. In the case of macromolecules (e.g. larger peptides and proteins), recent developments in the field of pulmonary delivery via the alveolar region of the lung have enabled the practical delivery of drugs such as insulin to blood circulation (see, e.g., Patton, J. S. et al., U.S. Pat. No. 5,997,848). Pulmonary delivery has the advantage of administration without needle injection, and obviates the need for potentially toxic penetration enhancers.

[0372] Compositions suitable for use in the invention include compositions wherein the active ingredients are contained in an effective amount to achieve the intended purpose. The determination of an effective dose is well within the capability of those skilled in the art.

[0373] Specialized forms of compositions may be prepared for direct intracellular delivery of macromolecules comprising CGDD or fragments thereof. For example, liposome preparations containing a cell-impermeable macromolecule may promote cell fusion and intracellular delivery of the macromolecule. Alternatively, CGDD or a fragment thereof may be joined to a short cationic N-terminal portion from the HIV Tat-1 protein. Fusion proteins thus generated have been found to transduce into the cells of all tissues, including the brain, in a mouse model system (Schwarze, S. R. et al. (1999) Science 285:1569-1572).

[0374] For any compound, the therapeutically effective dose can be estimated initially either in cell culture assays, e.g., of neoplastic cells, or in animal models such as mice, rats, rabbits, dogs, monkeys, or pigs. An animal model may also be used to determine the appropriate concentration range and route of administration. Such information can then be used to determine useful doses and routes for administration in humans.

[0375] A therapeutically effective dose refers to that amount of active ingredient, for example CGDD or fragments thereof, antibodies of CGDD, and agonists, antagonists or inhibitors of CGDD, which ameliorates the symptoms or condition. Therapeutic efficacy and toxicity may be determined by standard pharmaceutical procedures in cell cultures or with experimental animals, such as by calculating the ED₅₀ (the dose therapeutically effective in 50% of the population) or LD₅₀ (the dose lethal to 50% of the population) statistics. The dose ratio of toxic to therapeutic effects is the therapeutic index, which can be expressed as the LD₅₀/ED₅₀ ratio. Compositions which exhibit large therapeutic indices are preferred. The data obtained from cell culture assays and animal studies are used to formulate a range of dosage for human use. The dosage contained in such compositions is preferably within a range of circulating concentrations that includes the ED₅₀ with little or no toxicity. The dosage varies within this range depending upon the dosage form employed, the sensitivity of the patient, and the route of administration.

[0376] The exact dosage will be determined by the practitioner, in light of factors related to the subject requiring treatment. Dosage and administration are adjusted to provide sufficient levels of the active moiety or to maintain the desired effect. Factors which may be taken into account include the severity of the disease state, the general health of the subject, the age, weight, and gender of the subject, time and frequency of administration, drug combination(s), reaction sensitivities, and response to therapy. Long-acting compositions may be administered every 3 to 4 days, every week, or biweekly depending on the half-life and clearance rate of the particular formulation.

[0377] Normal dosage amounts may vary from about 0.1 μg to 100,000 μg, up to a total dose of about 1 gram, depending upon the route of administration. Guidance as to particular dosages and methods of delivery is provided in the literature and generally available to practitioners in the art. Those skilled in the art will employ different formulations for nucleotides than for proteins or their inhibitors. Similarly, delivery of polynucleotides or polypeptides will be specific to particular cells, conditions, locations, etc.

[0378] Diagnostics

[0379] In another embodiment, antibodies which specifically bind CGDD may be used for the diagnosis of disorders characterized by expression of CGDD, or in assays to monitor patients being treated with CGDD or agonists, antagonists, or inhibitors of CGDD. Antibodies useful for diagnostic purposes may be prepared in the same manner as described above for therapeutics. Diagnostic assays for CGDD include methods which utilize the antibody and a label to detect CGDD in human body fluids or in extracts of cells or tissues. The antibodies may be used with or without modification, and may be labeled by covalent or non-covalent attachment of a reporter molecule. A wide variety of reporter molecules, several of which are described above, are known in the art and may be used.

[0380] A variety of protocols for measuring CGDD, including ELISAs, RIAs, and FACS, are known in the art and provide a basis for diagnosing altered or abnormal levels of CGDD expression. Normal or standard values for CGDD expression are established by combining body fluids or cell extracts taken from normal mammalian subjects, for example, human subjects, with antibodies to CGDD under conditions suitable for complex formation. The amount of standard complex formation may be quantitated by various methods, such as photometric means. Quantities of CGDD expressed in subject, control, and disease samples from biopsied tissues are compared with the standard values. Deviation between standard and subject values establishes the parameters for diagnosing disease.

[0381] In another embodiment of the invention, the polynucleotides encoding CGDD may be used for diagnostic purposes. The polynucleotides which may be used include oligonucleotide sequences, complementary RNA and DNA molecules, and PNAs. The polynucleotides may be used to detect and quantify gene expression in biopsied tissues in which expression of CGDD may be correlated with disease. The diagnostic assay may be used to determine absence, presence, and excess expression of CGDD, and to monitor regulation of CGDD levels during therapeutic intervention.

[0382] In one aspect, hybridization with PCR probes which are capable of detecting polynucleotide sequences, including genomic sequences, encoding CGDD or closely related molecules may be used to identify nucleic acid sequences which encode CGDD. The specificity of the probe, whether it is made from a highly specific region, e.g., the 5′ regulatory region, or from a less specific region, e.g., a conserved motif, and the stringency of the hybridization or amplification will determine whether the probe identifies only naturally occurring sequences encoding CGDD, allelic variants, or related sequences.

[0383] Probes may also be used for the detection of related sequences, and may have at least 50% sequence identity to any of the CGDD encoding sequences. The hybridization probes of the subject invention may be DNA or RNA and may be derived from the sequence of SEQ ID NO:22-42 or from genomic sequences including promoters, enhancers, and introns of the CGDD gene.

[0384] Means for producing specific hybridization probes for DNAs encoding CGDD include the cloning of polynucleotide sequences encoding CGDD or CGDD derivatives into vectors for the production of mRNA probes. Such vectors are known in the art, are commercially available, and may be used to synthesize RNA probes in vitro by means of the addition of the appropriate RNA polymerases and the appropriate labeled nucleotides. Hybridization probes may be labeled by a variety of reporter groups, for example, by radionuclides such as ³²P or ³⁵S, or by enzymatic labels, such as alkaline phosphatase coupled to the probe via avidin/biotin coupling systems, and the like.

[0385] Polynucleotide sequences encoding CGDD may be used for the diagnosis of disorders associated with expression of CGDD. Examples of such disorders include, but are not limited to a cell proliferative disorder such as actinic keratosis, arteriosclerosis, atherosclerosis, bursitis, cirrhosis, hepatitis, mixed connective tissue disease (MCTD), myelofibrosis, paroxysmal nocturnal hemoglobinuria, polycythemia vera, psoriasis, primary thrombocythemia, and cancers including adenocarcinoma, leukemia, lymphoma, melanoma, myeloma, sarcoma, teratocarcinoma, and, in particular, cancers of the adrenal gland, bladder, bone, bone marrow, brain, breast, cervix, gall bladder, ganglia, gastrointestinal tract, heart, kidney, liver, lung, muscle, ovary, pancreas, parathyroid, penis, prostate, salivary glands, skin, spleen, testis, thymus, thyroid, and uterus; a developmental disorder such as renal tubular acidosis, anemia, Cushing's syndrome, achondroplastic dwarfism, Duchenne and Becker muscular dystrophy, epilepsy, gonadal dysgenesis, WAGR syndrome (Wilms' tumor, aniridia, genitourinary abnormalities, and mental retardation), Smith-Magenis syndrome, myelodysplastic syndrome, hereditary mucoepithelial dysplasia, hereditary keratodermas, hereditary neuropathies such as Charcot-Marie-Tooth disease and neurofibromatosis, hypothyroidism, hydrocephalus, seizure disorders such as Syndenham's chorea and cerebral palsy, spina bifida, anencephaly, craniorachischisis, congenital glaucoma, cataract, and sensorineural hearing loss; a neurological disorder such as epilepsy, ischemic cerebrovascular disease, stroke, cerebral neoplasms, Alzheimer's disease, Pick's disease, Huntington's disease, dementia, Parkinson's disease and other extrapyramidal disorders, amyotrophic lateral sclerosis and other motor neuron disorders, progressive neural muscular atrophy, retinitis pigmentosa, hereditary ataxias, multiple sclerosis and other demyelinating diseases, bacterial and viral meningitis, brain abscess, subdural empyema, epidural abscess, suppurative intracranial thrombophlebitis, myelitis and radiculitis, viral central nervous system disease, prion diseases including kuru, Creutzfeldt-Jakob disease, and Gerstmann-Straussler-Scheinker syndrome, fatal familial insomnia, nutritional and metabolic diseases of the nervous system, neurofibromatosis, tuberous sclerosis, cerebelloretinal hemangioblastomatosis, encephalotrigeminal syndrome, mental retardation and other developmental disorders of the central nervous system including Down syndrome, cerebral palsy, neuroskeletal disorders, autonomic nervous system disorders, cranial nerve disorders, spinal cord diseases, muscular dystrophy and other neuromuscular disorders, peripheral nervous system disorders, dermatomyositis and polymyositis, inherited, metabolic, endocrine, and toxic myopathies, myasthenia gravis, periodic paralysis, mental disorders including mood, anxiety, and schizophrenic disorders, seasonal affective disorder (SAD), akathesia, amnesia, catatonia, diabetic neuropathy, tardive dyskinesia, dystonias, paranoid psychoses, postherpetic neuralgia, Tourette's disorder, progressive supranuclear palsy, corticobasal degeneration, and familial frontotemporal dementia; an autoimmune/inflammatory disorder such as acquired immunodeficiency syndrome (AIDS), Addison's disease, adult respiratory distress syndrome, allergies, ankylosing spondylitis, amyloidosis, anemia, asthma, atherosclerosis, autoimmune hemolytic anemia, autoimmune thyroiditis, autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy (APECED), bronchitis, cholecystitis, contact dermatitis, Crohn's disease, atopic dermatitis, dermatomyositis, diabetes mellitus, emphysema, episodic lymphopenia with lymphocytotoxins, erythroblastosis fetalis, erythema nodosum, atrophic gastritis, glomerulonephritis, Goodpasture's syndrome, gout, Graves' disease, Hashimoto's thyroiditis, hypereosinophilia, irritable bowel syndrome, multiple sclerosis, myasthenia gravis, myocardial or pericardial inflammation, osteoarthritis, osteoporosis, pancreatitis, polymyositis, psoriasis, Reiter's syndrome, rheumatoid arthritis, scleroderma, Sjögren's syndrome, systemic anaphylaxis, systemic lupus erythematosus, systemic sclerosis, thrombocytopenic purpura, ulcerative colitis, uveitis, Werner syndrome, complications of cancer, hemodialysis, and extracorporeal circulation, viral, bacterial, fungal, parasitic, protozoal, and helminthic infections, and trauma; a reproductive disorder such as a disorder of prolactin production, infertility, including tubal disease, ovulatory defects, endometriosis, a disruption of the estrous cycle, a disruption of the menstrual cycle, polycystic ovary syndrome, ovarian hyperstimulation syndrome, an endometrial or ovarian tumor, a uterine fibroid, autoimmune disorders, ectopic pregnancy, teratogenesis; cancer of the breast, fibrocystic breast disease, galactorrhea; a disruption of spermatogenesis, abnormal sperm physiology, cancer of the testis, cancer of the prostate, benign prostatic hyperplasia, prostatitis, Peyronie's disease, impotence, carcinoma of the male breast, gynecomastia, hypergonadotropic and hypogonadotropic hypogonadism, pseudohermaphroditism, azoospermia, premature ovarian failure, acrosin deficiency, delayed puperty, retrograde ejaculation and anejaculation, haemangioblastomas, cystsphaeochromocytomas, paraganglioma, cystadenomas of the epididymis, and endolymphatic sac tumors; and a disorder of the placenta such as preeclampsia, choriocarcinoma, abruptio placentae, placenta previa, placental or maternal floor infarction, placenta accreta, increate, and percreta, extrachorial placentas, chorangioma, chorangiosis, chronic villitis, placental villous endema, widespread fibrosis of the terminal villi, intervillous thrombi, hemorraghic endovasculitis, erythroblastosis fetalis, and nonimmune fetal hydrops. The polynucleotide sequences encoding CGDD may be used in Southern or northern analysis, dot blot, or other membrane-based technologies; in PCR technologies; in dipstick, pin, and multiformat ELISA-like assays; and in microarrays utilizing fluids or tissues from patients to detect altered CGDD expression. Such qualitative or quantitative methods are well known in the art.

[0386] In a particular aspect, the nucleotide sequences encoding CGDD may be useful in assays that detect the presence of associated disorders, particularly those mentioned above. The nucleotide sequences encoding CGDD may be labeled by standard methods and added to a fluid or tissue sample from a patient under conditions suitable for the formation of hybridization complexes. After a suitable incubation period, the sample is washed and the signal is quantified and compared with a standard value. If the amount of signal in the patient sample is significantly altered in comparison to a control sample then the presence of altered levels of nucleotide sequences encoding CGDD in the sample indicates the presence of the associated disorder. Such assays may also be used to evaluate the efficacy of a particular therapeutic treatment regimen in animal studies, in clinical trials, or to monitor the treatment of an individual patient.

[0387] In order to provide a basis for the diagnosis of a disorder associated with expression of CGDD, a normal or standard profile for expression is established. This may be accomplished by combining body fluids or cell extracts taken from normal subjects, either animal or human, with a sequence, or a fragment thereof, encoding CGDD, under conditions suitable for hybridization or amplification. Standard hybridization may be quantified by comparing the values obtained from normal subjects with values from an experiment in which a known amount of a substantially purified polynucleotide is used. Standard values obtained in this manner may be compared with values obtained from samples from patients who are symptomatic for a disorder. Deviation from standard values is used to establish the presence of a disorder.

[0388] Once the presence of a disorder is established and a treatment protocol is initiated, hybridization assays may be repeated on a regular basis to determine if the level of expression in the patient begins to approximate that which is observed in the normal subject. The results obtained from successive assays may be used to show the efficacy of treatment over a period ranging from several days to months.

[0389] With respect to cancer, the presence of an abnormal amount of transcript (either under- or overexpressed) in biopsied tissue from an individual may indicate a predisposition for the development of the disease, or may provide a means for detecting the disease prior to the appearance of actual clinical symptoms. A more definitive diagnosis of this type may allow health professionals to employ preventative measures or aggressive treatment earlier thereby preventing the development or further progression of the cancer.

[0390] Additional diagnostic uses for oligonucleotides designed from the sequences encoding CGDD may involve the use of PCR. These oligomers may be chemically synthesized, generated enzymatically, or produced in vitro. Oligomers will preferably contain a fragment of a polynucleotide encoding CGDD, or a fragment of a polynucleotide complementary to the polynucleotide encoding CGDD, and will be employed under optimized conditions for identification of a specific gene or condition. Oligomers may also be employed under less stringent conditions for detection or quantification of closely related DNA or RNA sequences.

[0391] In a particular aspect, oligonucleotide primers derived from the polynucleotide sequences encoding CGDD may be used to detect single nucleotide polymorphisms (SNPs). SNPs are substitutions, insertions and deletions that are a frequent cause of inherited or acquired genetic disease in humans. Methods of SNP detection include, but are not limited to, single-stranded conformation polymorphism (SSCP) and fluorescent SSCP (fSSCP) methods. In SSCP, oligonucleotide primers derived from the polynucleotide sequences encoding CGDD are used to amplify DNA using the polymerase chain reaction (PCR). The DNA may be derived, for example, from diseased or normal tissue, biopsy samples, bodily fluids, and the like. SNPs in the DNA cause differences in the secondary and tertiary structures of PCR products in single-stranded form, and these differences are detectable using gel electrophoresis in non-denaturing gels. In fSCCP, the oligonucleotide primers are fluorescently labeled, which allows detection of the amplimers in high-throughput equipment such as DNA sequencing machines. Additionally, sequence database analysis methods, termed in silico SNP (isSNP), are capable of identifying polymorphisms by comparing the sequence of individual overlapping DNA fragments which assemble into a common consensus sequence. These computer-based methods filter out sequence variations due to laboratory preparation of DNA and sequencing errors using statistical models and automated analyses of DNA sequence chromatograms. In the alternative, SNPs may be detected and characterized by mass spectrometry using, for example, the high throughput MASSARRAY system (Sequenom, Inc., San Diego Calif.).

[0392] SNPs may be used to study the genetic basis of human disease. For example, at least 16 common SNPs have been associated with non-insulin-dependent diabetes mellitus. SNPs are also useful for examining differences in disease outcomes in monogenic disorders, such as cystic fibrosis, sickle cell anemia, or chronic granulomatous disease. For example, variants in the mannose-binding lectin, MBL2, have been shown to be correlated with deleterious pulmonary outcomes in cystic fibrosis. SNPs also have utility in pharmacogenomics, the identification of genetic variants that influence a patient's response to a drug, such as life-threatening toxicity. For example, a variation in N-acetyl transferase is associated with a high incidence of peripheral neuropathy in response to the anti-tuberculosis drug isoniazid, while a variation in the core promoter of the ALOX5 gene results in diminished clinical response to treatment with an anti-asthma drug that targets the 5-lipoxygenase pathway. Analysis of the distribution of SNPs in different populations is useful for investigating genetic drift, mutation, recombination, and selection, as well as for tracing the origins of populations and their migrations. (Taylor, J. G. et al. (2001) Trends Mol. Med. 7:507-512; Kwok, P.-Y. and Z. Gu (1999) Mol. Med. Today 5:538-543; Nowotny, P. et al. (2001) Curr. Opin. Neurobiol. 11:637-641.)

[0393] Methods which may also be used to quantify the expression of CGDD include radiolabeling or biotinylating nucleotides, coamplification of a control nucleic acid, and interpolating results from standard curves. (See, e.g., Melby, P. C. et al. (1993) J. Immunol. Methods 159:235-244; Duplaa, C. et al. (1993) Anal. Biochem. 212:229-236.) The speed of quantitation of multiple samples may be accelerated by running the assay in a high-throughput format where the oligomer or polynucleotide of interest is presented in various dilutions and a spectrophotometric or colorimetric response gives rapid quantitation.

[0394] In further embodiments, oligonucleotides or longer fragments derived from any of the polynucleotide sequences described herein may be used as elements on a microarray. The microarray can be used in transcript imaging techniques which monitor the relative expression levels of large numbers of genes simultaneously as described below. The microarray may also be used to identify genetic variants, mutations, and polymorphisms. This information may be used to determine gene function, to understand the genetic basis of a disorder, to diagnose a disorder, to monitor progression/regression of disease as a function of gene expression, and to develop and monitor the activities of therapeutic agents in the treatment of disease. In particular, this information may be used to develop a pharmacogenomic profile of a patient in order to select the most appropriate and effective treatment regimen for that patient. For example, therapeutic agents which are highly effective and display the fewest side effects may be selected for a patient based on his/her pharmacogenomic profile.

[0395] In another embodiment, CGDD, fragments of CGDD, or antibodies specific for CGDD may be used as elements on a microarray. The microarray may be used to monitor or measure protein-protein interactions, drug-target interactions, and gene expression profiles, as described above.

[0396] A particular embodiment relates to the use of the polynucleotides of the present invention to generate a transcript image of a tissue or cell type. A transcript image represents the global pattern of gene expression by a particular tissue or cell type. Global gene expression patterns are analyzed by quantifying the number of expressed genes and their relative abundance under given conditions and at a given time. (See Seilhamer et al., “Comparative Gene Transcript Analysis,” U.S. Pat. No. 5,840,484, expressly incorporated by reference herein.) Thus a transcript image may be generated by hybridizing the polynucleotides of the present invention or their complements to the totality of transcripts or reverse transcripts of a particular tissue or cell type. In one embodiment, the hybridization takes place in high-throughput format, wherein the polynucleotides of the present invention or their complements comprise a subset of a plurality of elements on a microarray. The resultant transcript image would provide a profile of gene activity.

[0397] Transcript images may be generated using transcripts isolated from tissues, cell lines, biopsies, or other biological samples. The transcript image may thus reflect gene expression in vivo, as in the case of a tissue or biopsy sample, or in vitro, as in the case of a cell line.

[0398] Transcript images which profile the expression of the polynucleotides of the present invention may also be used in conjunction with in vitro model systems and preclinical evaluation of pharmaceuticals, as well as toxicological testing of industrial and naturally-occurring environmental compounds. All compounds induce characteristic gene expression patterns, frequently termed molecular fingerprints or toxicant signatures, which are indicative of mechanisms of action and toxicity (Nuwaysir, E. F. et al. (1999) Mol. Carcinog. 24:153-159; Steiner, S. and N. L. Anderson (2000) Toxicol. Lett. 112-113:467-471, expressly incorporated by reference herein). If a test compound has a signature similar to that of a compound with known toxicity, it is likely to share those toxic properties. These fingerprints or signatures are most useful and refined when they contain expression information from a large number of genes and gene families. Ideally, a genome-wide measurement of expression provides the highest quality signature. Even genes whose expression is not altered by any tested compounds are important as well, as the levels of expression of these genes are used to normalize the rest of the expression data. The normalization procedure is useful for comparison of expression data after treatment with different compounds. While the assignment of gene function to elements of a toxicant signature aids in interpretation of toxicity mechanisms, knowledge of gene function is not necessary for the statistical matching of signatures which leads to prediction of toxicity. (See, for example, Press Release 00-02 from the National Institute of Environmental Health Sciences, released Feb. 29, 2000, available at http://www.niehs.nih.gov/oc/news/toxchip.htm.) Therefore, it is important and desirable in toxicological screening using toxicant signatures to include all expressed gene sequences.

[0399] In one embodiment, the toxicity of a test compound is assessed by treating a biological sample containing nucleic acids with the test compound. Nucleic acids that are expressed in the treated biological sample are hybridized with one or more probes specific to the polynucleotides of the present invention, so that transcript levels corresponding to the polynucleotides of the present invention may be quantified. The transcript levels in the treated biological sample are compared with levels in an untreated biological sample. Differences in the transcript levels between the two samples are indicative of a toxic response caused by the test compound in the treated sample.

[0400] Another particular embodiment relates to the use of the polypeptide sequences of the present invention to analyze the proteome of a tissue or cell type. The term proteome refers to the global pattern of protein expression in a particular tissue or cell type. Each protein component of a proteome can be subjected individually to further analysis. Proteome expression patterns, or profiles, are analyzed by quantifying the number of expressed proteins and their relative abundance under given conditions and at a given time. A profile of a cell's proteome may thus be generated by separating and analyzing the polypeptides of a particular tissue or cell type. In one embodiment, the separation is achieved using two-dimensional gel electrophoresis, in which proteins from a sample are separated by isoelectric focusing in the first dimension, and then according to molecular weight by sodium dodecyl sulfate slab gel electrophoresis in the second dimension (Steiner and Anderson, supra). The proteins are visualized in the gel as discrete and uniquely positioned spots, typically by staining the gel with an agent such as Coomassie Blue or silver or fluorescent stains. The optical density of each protein spot is generally proportional to the level of the protein in the sample. The optical densities of equivalently positioned protein spots from different samples, for example, from biological samples either treated or untreated with a test compound or therapeutic agent, are compared to identify any changes in protein spot density related to the treatment. The proteins in the spots are partially sequenced using, for example, standard methods employing chemical or enzymatic cleavage followed by mass spectrometry. The identity of the protein in a spot may be determined by comparing its partial sequence, preferably of at least 5 contiguous amino acid residues, to the polypeptide sequences of the present invention. In some cases, further sequence data may be obtained for definitive protein identification.

[0401] A proteomic profile may also be generated using antibodies specific for CGDD to quantify the levels of CGDD expression. In one embodiment, the antibodies are used as elements on a microarray, and protein expression levels are quantified by exposing the microarray to the sample and detecting the levels of protein bound to each array element (tucking, A. et al. (1999) Anal. Biochem. 270:103-111; Mendoze, L. G. et al. (1999) Biotechniques 27:778-788). Detection maybe performed by a variety of methods known in the art, for example, by reacting the proteins in the sample with a thiol- or amino-reactive fluorescent compound and detecting the amount of fluorescence bound at each array element.

[0402] Toxicant signatures at the proteome level are also useful for toxicological screening, and should be analyzed in parallel with toxicant signatures at the transcript level. There is a poor correlation between transcript and protein abundances for some proteins in some tissues (Anderson, N. L. and J. Seilhamer (1997) Electrophoresis 18:533-537), so proteome toxicant signatures may be useful in the analysis of compounds which do not significantly affect the transcript image, but which alter the proteomic profile. In addition, the analysis of transcripts in body fluids is difficult, due to rapid degradation of mRNA, so proteomic profiling may be more reliable and informative in such cases.

[0403] In another embodiment, the toxicity of a test compound is assessed by treating a biological sample containing proteins with the test compound. Proteins that are expressed in the treated biological sample are separated so that the amount of each protein can be quantified. The amount of each protein is compared to the amount of the corresponding protein in an untreated biological sample. A difference in the amount of protein between the two samples is indicative of a toxic response to the test compound in the treated sample. Individual proteins are identified by sequencing the amino acid residues of the individual proteins and comparing these partial sequences to the polypeptides of the present invention.

[0404] In another embodiment, the toxicity of a test compound is assessed by treating a biological sample containing proteins with the test compound. Proteins from the biological sample are incubated with antibodies specific to the polypeptides of the present invention. The amount of protein recognized by the antibodies is quantified. The amount of protein in the treated biological sample is compared with the amount in an untreated biological sample. A difference in the amount of protein between the two samples is indicative of a toxic response to the test compound in the treated sample.

[0405] Microarrays may be prepared, used, and analyzed using methods known in the art. (See, e.g., Brennan, T. M. et al. (1995) U.S. Pat. No. 5,474,796; Schena, M. et al. (1996) Proc. Natl. Acad. Sci. USA 93:10614-10619; Baldeschweiler et al. (1995) PCT application WO95/251116; Shalon, D. et al. (1995) PCT application WO95/35505; Heller, R. A. et al. (1997) Proc. Natl. Acad. Sci. USA 94:2150-2155; and Heller, M. J. et al. (1997) U.S. Pat. No. 5,605,662.) Various types of microarrays are well known and thoroughly described in DNA Microarrays: A Practical Approach, M. Schena, ed. (1999) Oxford University Press, London, hereby expressly incorporated by reference.

[0406] In another embodiment of the invention, nucleic acid sequences encoding CGDD may be used to generate hybridization probes useful in mapping the naturally occurring genomic sequence. Either coding or noncoding sequences may be used, and in some instances, noncoding sequences may be preferable over coding sequences. For example, conservation of a coding sequence among members of a multi-gene family may potentially cause undesired cross hybridization during chromosomal mapping. The sequences may be mapped to a particular chromosome, to a specific region of a chromosome, or to artificial chromosome constructions, e.g., human artificial chromosomes (HACs), yeast artificial chromosomes (YACs), bacterial artificial chromosomes (BACs), bacterial P1 constructions, or single chromosome cDNA libraries. (See, e.g., Harrington, J. J. et al. (1997) Nat. Genet. 15:345-355; Price, C. M. (1993) Blood Rev. 7:127-134; and Trask, B. J. (1991) Trends Genet. 7:149-154.) Once mapped, the nucleic acid sequences of the invention may be used to develop genetic linkage maps, for example, which correlate the inheritance of a disease state with the inheritance of a particular chromosome region or restriction fragment length polymorphism (RFLP). (See, for example, Lander, E. S. and D. Botstein (1986) Proc. Natl. Acad. Sci. USA 83:7353-7357.)

[0407] Fluorescent in situ hybridization (FISH) may be correlated with other physical and genetic map data. (See, e.g., Heinz-Ulrich, et al. (1995) in Meyers, supra, pp. 965-968.) Examples of genetic map data can be found in various scientific journals or at the Online Mendelian Inheritance in Man (OMIM) World Wide Web site. Correlation between the location of the gene encoding CGDD on a physical map and a specific disorder, or a predisposition to a specific disorder, may help define the region of DNA associated with that disorder and thus may further positional cloning efforts.

[0408] In situ hybridization of chromosomal preparations and physical mapping techniques, such as linkage analysis using established chromosomal markers, may be used for extending genetic maps. Often the placement of a gene on the chromosome of another mammalian species, such as mouse, may reveal associated markers even if the exact chromosomal locus is not known. This information is valuable to investigators searching for disease genes using positional cloning or other gene discovery techniques. Once the gene or genes responsible for a disease or syndrome have been crudely localized by genetic linkage to a particular genomic region, e.g., ataxia-telangiectasia to 11q22-23, any sequences mapping to that area may represent associated or regulatory genes for further investigation. (See, e.g., Gatti, R. A. et al. (1988) Nature 336:577-580.) The nucleotide sequence of the instant invention may also be used to detect differences in the chromosomal location due to translocation, inversion, etc., among normal, carrier, or affected individuals.

[0409] In another embodiment of the invention, CGDD, its catalytic or immunogenic fragments, or oligopeptides thereof can be used for screening libraries of compounds in any of a variety of drug screening techniques. The fragment employed in such screening may be free in solution, affixed to a solid support, borne on a cell surface, or located intracellularly. The formation of binding complexes between CGDD and the agent being tested may be measured.

[0410] Another technique for drug screening provides for high throughput screening of compounds having suitable binding affinity to the protein of interest. (See, e.g., Geysen, et al. (1984) PCT application WO84/03564.) In this method, large numbers of different small test compounds are synthesized on a solid substrate. The test compounds are reacted with CGDD, or fragments thereof, and washed. Bound CGDD is then detected by methods well known in the art. Purified CGDD can also be coated directly onto plates for use in the aforementioned drug screening techniques. Alternatively, non-neutralizing antibodies can be used to capture the peptide and immobilize it on a solid support.

[0411] In another embodiment, one may use competitive drug screening assays in which neutralizing antibodies capable of binding CGDD specifically compete with a test compound for binding CGDD. In this manner, antibodies can be used to detect the presence of any peptide which shares one or more antigenic determinants with CGDD.

[0412] In additional embodiments, the nucleotide sequences which encode CGDD may be used in any molecular biology techniques that have yet to be developed, provided the new techniques rely on properties of nucleotide sequences that are currently known, including, but not limited to, such properties as the triplet genetic code and specific base pair interactions.

[0413] Without further elaboration, it is believed that one skilled in the art can, using the preceding description, utilize the present invention to its fullest extent. The following embodiments are, therefore, to be construed as merely illustrative, and not limitative of the remainder of the disclosure in any way whatsoever.

[0414] The disclosures of all patents, applications and publications, mentioned above and below, including U.S. Ser. No. 60/286,820, U.S. Ser. No. 60/293,727, U.S. Ser. No. 60/283,294, U.S. Ser. No. 60/282,110, U.S. Ser. No. 60/287,228, U.S. Ser. No. 60/291,846, U.S. Ser. No. 60/291,662, U.S. Ser. No. 60/295,340, U.S. Ser. No. 60/295,263, and U.S. Ser. No. 60/349,705, are expressly incorporated by reference herein.

EXAMPLES

[0415] I. Construction of cDNA Libraries

[0416] Incyte cDNAs were derived from cDNA libraries described in the LIFESEQ GOLD database (Incyte Genomics, Palo Alto Calif.). Some tissues were homogenized and lysed in guanidinium isothiocyanate, while others were homogenized and lysed in phenol or in a suitable mixture of denaturants, such as TRIZOL (Life Technologies), a monophasic solution of phenol and guanidine isothiocyanate. The resulting lysates were centrifuged over CsCl cushions or extracted with chloroform. RNA was precipitated from the lysates with either isopropanol or sodium acetate and ethanol, or by other routine methods.

[0417] Phenol extraction and precipitation of RNA were repeated as necessary to increase RNA purity. In some cases, RNA was treated with DNase. For most libraries, poly(A)+ RNA was isolated using oligo d(T)-coupled paramagnetic particles (Promega), OLIGOTEX latex particles (QIAGEN, Chatsworth Calif.), or an OLIGOTEX mRNA purification kit (QIAGEN). Alternatively, RNA was isolated directly from tissue lysates using other RNA isolation kits, e.g., the POLY(A)PURE mRNA purification kit (Ambion, Austin Tex.).

[0418] In some cases, Stratagene was provided with RNA and constructed the corresponding cDNA libraries. Otherwise, cDNA was synthesized and cDNA libraries were constructed with the UNIZAP vector system (Stratagene) or SUPERSCRIPT plasmid system (Life Technologies), using the recommended procedures or similar methods known in the art. (See, e.g., Ausubel, 1997, supra, units 5.1-6.6.) Reverse transcription was initiated using oligo d(T) or random primers. Synthetic oligonucleotide adapters were ligated to double stranded cDNA, and the cDNA was digested with the appropriate restriction enzyme or enzymes. For most libraries, the cDNA was size-selected (300-1000 bp) using SEPHACRYL S1000, SEPHAROSE CL2B, or SEPHAROSE CL4B column chromatography (Amersham Pharmacia Biotech) or preparative agarose gel electrophoresis. cDNAs were ligated into compatible restriction enzyme sites of the polylinker of a suitable plasmid, e.g., PBLUESCRIPT plasmid (Stratagene), PSPORT1 plasmid (Life Technologies), PCDNA2.1 plasmid (Invitrogen, Carlsbad Calif.), PBK-CMV plasmid (Stratagene), PCR2-TOPOTA plasmid (Invitrogen), PCMV-ICIS plasmid (Stratagene), pIGEN (Incyte Genomics, Palo Alto Calif.), pRARE (Incyte Genomics), or pINCY (Incyte Genomics), or derivatives thereof. Recombinant plasmids were transformed into competent E. coli cells including XL1-Blue, XL1-BlueMRF, or SOLR from Stratagene or DH5α, DH10B, or ElectroMAX DH10B from Life Technologies.

[0419] II. Isolation of cDNA Clones

[0420] Plasmids obtained as described in Example I were recovered from host cells by in vivo excision using the UNIZAP vector system (Stratagene) or by cell lysis. Plasmids were purified using at least one of the following: a Magic or WIZARD Minipreps DNA purification system (Promega); an AGTC Miniprep purification kit (Edge Biosystems, Gaithersburg Md.); and QIAWELL 8 Plasmid, QIAWELL 8 Plus Plasmid, QIAWELL 8 Ultra Plasmid purification systems or the R.E.A.L. PREP 96 plasmid purification kit from QIAGEN. Following precipitation, plasmids were resuspended in 0.1 ml of distilled water and stored, with or without lyophilization, at 4° C.

[0421] Alternatively, plasmid DNA was amplified from host cell lysates using direct link PCR in a high-throughput format (Rao, V. B. (1994) Anal. Biochem. 216:1-14). Host cell lysis and thermal cycling steps were carried out in a single reaction mixture. Samples were processed and stored in 384-well plates, and the concentration of amplified plasmid DNA was quantified fluorometrically using PICOGREEN dye (Molecular Probes, Eugene Oreg.) and a FLUOROSKAN II fluorescence scanner (Labsystems Oy, Helsinki, Finland).

[0422] III. Sequencing and Analysis

[0423] Incyte cDNA recovered in plasmids as described in Example II were sequenced as follows. Sequencing reactions were processed using standard methods or high-throughput instrumentation such as the ABI CATALYST 800 (Applied Biosystems) thermal cycler or the PTC-200 thermal cycler (MJ Research) in conjunction with the HYDRA microdispenser (Robbins Scientific) or the MICROLAB 2200 (Hamilton) liquid transfer system. cDNA sequencing reactions were prepared using reagents provided by Amersham Pharmacia Biotech or supplied in ABI sequencing kits such as the ABI PRISM BIGDYE Terminator cycle sequencing ready reaction kit (Applied Biosystems). Electrophoretic separation of cDNA sequencing reactions and detection of labeled polynucleotides were carried out using the MEGABACE 1000 DNA sequencing system (Molecular Dynamics); the ABI PRISM 373 or 377 sequencing system (Applied Biosystems) in conjunction with standard ABI protocols and base calling software; or other sequence analysis systems known in the art. Reading frames within the cDNA sequences were identified using standard methods (reviewed in Ausubel, 1997, supra, unit 7.7). Some of the cDNA sequences were selected for extension using the techniques disclosed in Example VIII.

[0424] The polynucleotide sequences derived from Incyte cDNAs were validated by removing vector, linker, and poly(A) sequences and by masking ambiguous bases, using algorithms and programs based on BLAST, dynamic programming, and dinucleotide nearest neighbor analysis. The Incyte cDNA sequences or translations thereof were then queried against a selection of public databases such as the GenBank primate, rodent, mammalian, vertebrate, and eukaryote databases and BLOCKS, PRINTS, DOMO, PRODOM; PROTEOME databases with sequences from Homo sapiens, Rattus norvegicus, Mus musculus, Caenorhabditis elegans, Saccharomyces cerevisiae, Schizosaccharomyces pombe, and Candida albicans (Incyte Genomics, Palo Alto Calif.); hidden Markov model (HMM)-based protein family databases such as PFAM, INCY, and TIGRFAM (Haft, D. H. et al. (2001) Nucleic Acids Res. 29:41-43); and HMM-based protein domain databases such as SMART (Schultz et al. (1998) Proc. Natl. Acad. Sci. USA 95:5857-5864; Letunic, I. et al. (2002) Nucleic Acids Res. 30:242-244). (HMM is a probabilistic approach which analyzes consensus primary structures of gene families. See, for example, Eddy, S. R. (1996) Curr. Opin. Struct. Biol. 6:361-365.) The queries were performed using programs based on BLAST, FASTA, BLIMPS, and HMMER. The Incyte cDNA sequences were assembled to produce full length polynucleotide sequences. Alternatively, GenBank cDNAs, GenBank ESTs, stitched sequences, stretched sequences, or Genscan-predicted coding sequences (see Examples IV and V) were used to extend Incyte cDNA assemblages to full length. Assembly was performed using programs based on Phred, Phrap, and Consed, and cDNA assemblages were screened for open reading frames using programs based on GeneMark, BLAST, and FASTA. The full length polynucleotide sequences were translated to derive the corresponding full length polypeptide sequences. Alternatively, a polypeptide of the invention may begin at any of the methionine residues of the full length translated polypeptide. Full length polypeptide sequences were subsequently analyzed by querying against databases such as the GenBank protein databases (genpept), SwissProt, the PROTEOME databases, BLOCKS, PRINTS, DOMO, PRODOM, Prosite, hidden Markov model (HMM)-based protein family databases such as PFAM, INCY, and TIGRFAM; and HMM-based protein domain databases such as SMART. Full length polynucleotide sequences are also analyzed using MACDNASIS PRO software (Hitachi Software Engineering, South San Francisco Calif.) and LASERGENE software (DNASTAR). Polynucleotide and polypeptide sequence alignments are generated using default parameters specified by the CLUSTAL algorithm as incorporated into the MEGALIGN multisequence alignment program (DNASTAR), which also calculates the percent identity between aligned sequences.

[0425] Table 7 summarizes the tools, programs, and algorithms used for the analysis and assembly of Incyte cDNA and full length sequences and provides applicable descriptions, references, and threshold parameters. The first column of Table 7 shows the tools, programs, and algorithms used, the second column provides brief descriptions thereof, the third column presents appropriate references, all of which are incorporated by reference herein in their entirety, and the fourth column presents, where applicable, the scores, probability values, and other parameters used to evaluate the strength of a match between two sequences (the higher the score or the lower the probability value, the greater the identity between two sequences).

[0426] The programs described above for the assembly and analysis of full length polynucleotide and polypeptide sequences were also used to identify polynucleotide sequence fragments from SEQ ID NO:22-42. Fragments from about 20 to about 4000 nucleotides which are useful in hybridization and amplification technologies are described in Table 4, column 2.

[0427] IV. Identification and Editing of Coding Sequences from Genomic DNA

[0428] Putative proteins associated with cell growth, differentiation, and death were initially identified by running the Genscan gene identification program against public genomic sequence databases (e.g., gbpri and gbhtg). Genscan is a general-purpose gene identification program which analyzes genomic DNA sequences from a variety of organisms (See Burge, C. and S. Karlin (1997) J. Mol. Biol. 268:78-94, and Burge, C. and S. Karlin (1998) Curr. Opin. Struct. Biol. 8:346-354). The program concatenates predicted exons to form an assembled cDNA sequence extending from a methionine to a stop codon. The output of Genscan is a FASTA database of polynucleotide and polypeptide sequences. The maximum range of sequence for Genscan to analyze at once was set to 30 kb. To determine which of these Genscan predicted cDNA sequences encode proteins associated with cell growth, differentiation, and death, the encoded polypeptides were analyzed by querying against PFAM models for proteins associated with cell growth, differentiation, and death. Potential proteins associated with cell growth, differentiation, and death were also identified by homology to Incyte cDNA sequences that had been annotated as proteins associated with cell growth, differentiation, and death. These selected Genscan-predicted sequences were then compared by BLAST analysis to the genpept and gbpri public databases. Where necessary, the Genscan-predicted sequences were then edited by comparison to the top BLAST hit from genpept to correct errors in the sequence predicted by Genscan, such as extra or omitted exons. BLAST analysis was also used to find any Incyte cDNA or public cDNA coverage of the Genscan-predicted sequences, thus providing evidence for transcription. When Incyte cDNA coverage was available, this information was used to correct or confirm the Genscan predicted sequence. Full length polynucleotide sequences were obtained by assembling Genscan-predicted coding sequences with Incyte cDNA sequences and/or public cDNA sequences using the assembly process described in Example m. Alternatively, full length polynucleotide sequences were derived entirely from edited or unedited Genscan-predicted coding sequences.

[0429] V. Assembly of Genomic Sequence Data with cDNA Sequence Data “Stitched” Sequences

[0430] Partial cDNA sequences were extended with exons predicted by the Genscan gene identification program described in Example IV. Partial cDNAs assembled as described in Example III were mapped to genomic DNA and parsed into clusters containing related cDNAs and Genscan exon predictions from one or more genomic sequences. Each cluster was analyzed using an algorithm based on graph theory and dynamic programming to integrate cDNA and genomic information, generating possible splice variants that were subsequently confirmed, edited, or extended to create a full length sequence. Sequence intervals in which the entire length of the interval was present on more than one sequence in the cluster were identified, and intervals thus identified were considered to be equivalent by transitivity. For example, if an interval was present on a cDNA and two genomic sequences, then all three intervals were considered to be equivalent. This process allows unrelated but consecutive genomic sequences to be brought together, bridged by cDNA sequence. Intervals thus identified were then “stitched” together by the stitching algorithm in the order that they appear along their parent sequences to generate the longest possible sequence, as well as sequence variants. Linkages between intervals which proceed along one type of parent sequence (cDNA to cDNA or genomic sequence to genomic sequence) were given preference over linkages which change parent type (cDNA to genomic sequence). The resultant stitched sequences were translated and compared by BLAST analysis to the genpept and gbpri public databases. Incorrect exons predicted by Genscan were corrected by comparison to the top BLAST hit from genpept. Sequences were further extended with additional cDNA sequences, or by inspection of genomic DNA, when necessary.

[0431] “Stretched” Sequences

[0432] Partial DNA sequences were extended to full length with an algorithm based on BLAST analysis. First, partial cDNAs assembled as described in Example III were queried against public databases such as the GenBank primate, rodent, mammalian, vertebrate, and eukaryote databases using the BLAST program. The nearest GenBank protein homolog was then compared by BLAST analysis to either Incyte cDNA sequences or GenScan exon predicted sequences described in Example IV. A chimeric protein was generated by using the resultant high-scoring segment pairs (HSPs) to map the translated sequences onto the GenBank protein homolog. Insertions or deletions may occur in the chimeric protein with respect to the original GenBank protein homolog. The GenBank protein homolog, the chimeric protein, or both were used as probes to search for homologous genomic sequences from the public human genome databases. Partial DNA sequences were therefore “stretched” or extended by the addition of homologous genomic sequences. The resultant stretched sequences were examined to determine whether it contained a complete gene.

[0433] VI. Chromosomal Mapping of CGDD Encoding Polynucleotides

[0434] The sequences which were used to assemble SEQ ID NO:22-42 were compared with sequences from the Incyte LIFESEQ database and public domain databases using BLAST and other implementations of the Smith-Waterman algorithm. Sequences from these databases that matched SEQ ID NO:22-42 were assembled into clusters of contiguous and overlapping sequences using assembly algorithms such as Phrap (Table 7). Radiation hybrid and genetic mapping data available from public resources such as the Stanford Human Genome Center (SHGC), Whitehead Institute for Genome Research (WIGR), and Généthon were used to determine if any of the clustered sequences had been previously mapped. Inclusion of a mapped sequence in a cluster resulted in the assignment of all sequences of that cluster, including its particular SEQ ID NO:, to that map location.

[0435] Map locations are represented by ranges, or intervals, of human chromosomes. The map position of an interval, in centiMorgans, is measured relative to the terminus of the chromosome's p-arm. (The centimorgan (cM) is a unit of measurement based on recombination frequencies between chromosomal markers. On average, 1 cM is roughly equivalent to 1 megabase (Mb) of DNA in humans, although this can vary widely due to hot and cold spots of recombination.) The cM distances are based on genetic markers mapped by Généthon which provide boundaries for radiation hybrid markers whose sequences were included in each of the clusters. Human genome maps and other resources available to the public, such as the NCBI “GeneMap'99” World Wide Web site (http://www.ncbi.nlm.nih.gov/genemap/), can be employed to determine if previously identified disease genes map within or in proximity to the intervals indicated above.

[0436] In this manner, SEQ ID NO:26 was mapped to chromosome 3 within the interval from 63.30 to 77.40 centiMorgans.

[0437] VII. Analysis of Polynucleotide Expression

[0438] Northern analysis is a laboratory technique used to detect the presence of a transcript of a gene and involves the hybridization of a labeled nucleotide sequence to a membrane on which RNAs from a particular cell type or tissue have been bound. (See, e.g., Sambrook, supra, ch. 7; Ausubel (1995) supra, ch. 4 and 16.)

[0439] Analogous computer techniques applying BLAST were used to search for identical or related molecules in cDNA databases such as GenBank or LIFESEQ (Incyte Genomics). This analysis is much faster than multiple membrane-based hybridizations. In addition, the sensitivity of the computer search can be modified to determine whether any particular match is categorized as exact or similar. The basis of the search is the product score, which is defined as: $\frac{{BLAST}\quad {Score} \times {Percent}\quad {Identity}}{5 \times {minimum}\quad \left\{ {{{length}\left( {{Seq}{.1}} \right)},{{length}\left( {{Seq}{.2}} \right)}} \right\}}$

[0440] The product score takes into account both the degree of similarity between two sequences and the length of the sequence match. The product score is a normalized value between 0 and 100, and is calculated as follows: the BLAST score is multiplied by the percent nucleotide identity and the product is divided by (5 times the length of the shorter of the two sequences). The BLAST score is calculated by assigning a score of +5 for every base that matches in a high-scoring segment pair (HSP), and −4 for every mismatch. Two sequences may share more than one HSP (separated by gaps). If there is more than one HSP, then the pair with the highest BLAST score is used to calculate the product score. The product score represents a balance between fractional overlap and quality in a BLAST alignment. For example, a product score of 100 is produced only for 100% identity over the entire length of the shorter of the two sequences being compared. A product score of 70 is produced either by 100% identity and 70% overlap at one end, or by 88% identity and 100% overlap at the other. A product score of 50 is produced either by 100% identity and 50% overlap at one end, or 79% identity and 100% overlap.

[0441] Alternatively, polynucleotide sequences encoding CGDD are analyzed with respect to the tissue sources from which they were derived. For example, some full length sequences are assembled, at least in part, with overlapping Incyte cDNA sequences (see Example III). Each cDNA sequence is derived from a cDNA library constructed from a human tissue. Each human tissue is classified into one of the following organ/tissue categories: cardiovascular system; connective tissue; digestive system; embryonic structures; endocrine system; exocrine glands; genitalia, female; genitalia, male; germ cells; hemic and immune system; liver; musculoskeletal system; nervous system; pancreas; respiratory system; sense organs; skin; stomatognathic system; unclassified/mixed; or urinary tract. The number of libraries in each category is counted and divided by the total number of libraries across all categories. Similarly, each human tissue is classified into one of the following disease/condition categories: cancer, cell line, developmental, inflammation, neurological, trauma, cardiovascular, pooled, and other, and the number of libraries in each category is counted and divided by the total number of libraries across all categories. The resulting percentages reflect the tissue- and disease-specific expression of cDNA encoding CGDD. cDNA sequences and cDNA library/tissue information are found in the LIFESEQ GOLD database (Incyte Genomics, Palo Alto Calif.).

[0442] VIII. Extension of CGDD Encoding Polynucleotides

[0443] Full length polynucleotide sequences were also produced by extension of an appropriate fragment of the full length molecule using oligonucleotide primers designed from this fragment. One primer was synthesized to initiate 5′ extension of the known fragment, and the other primer was synthesized to initiate 3′ extension of the known fragment. The initial primers were designed using OLIGO 4.06 software (National Biosciences), or another appropriate program, to be about 22 to 30 nucleotides in length, to have a GC content of about 50% or more, and to anneal to the target sequence at temperatures of about 68° C. to about 72° C. Any stretch of nucleotides which would result in hairpin structures and primer-primer dimerizations was avoided.

[0444] Selected human cDNA libraries were used to extend the sequence. If more than one extension was necessary or desired, additional or nested sets of primers were designed.

[0445] High fidelity amplification was obtained by PCR using methods well known in the art. PCR was performed in 96-well plates using the PTC-200 thermal cycler (MJ Research, Inc.). The reaction nix contained DNA template, 200 nmol of each primer, reaction buffer containing Mg²⁺, (NH₄)₂SO₄, and 2-mercaptoethanol, Taq DNA polymerase (Amersham Pharmacia Biotech), ELONGASE enzyme (Life Technologies), and Pfu DNA polymerase (Stratagene), with the following parameters for primer pair PCI A and PCI B: Step 1: 94° C., 3 min; Step 2: 94° C., 15 sec; Step 3: 60° C., 1 min; Step 4: 68° C., 2 min; Step 5: Steps 2, 3, and 4 repeated 20 times; Step 6: 68° C., 5 min; Step 7: storage at 4° C. In the alternative, the parameters for primer pair T7 and SK+ were as follows: Step 1: 94° C., 3 min; Step 2: 94° C., 15 sec; Step 3: 57° C., 1 min; Step 4: 68° C., 2 min; Step 5: Steps 2, 3, and 4 repeated 20 times; Step 6: 68° C., 5 min; Step 7: storage at 4° C.

[0446] The concentration of DNA in each well was determined by dispensing 100 μl PICOGREEN quantitation reagent (0.25% (v/v) PICOGREEN; Molecular Probes, Eugene Oreg.) dissolved in 1×TE and 0.5 μl of undiluted PCR product into each well of an opaque fluorimeter plate (Corning Costar, Acton Mass.), allowing the DNA to bind to the reagent. The plate was scanned in a Fluoroskan II (Labsystems Oy, Helsinki, Finland) to measure the fluorescence of the sample and to quantify the concentration of DNA. A 5 μl to 10 μl aliquot of the reaction mixture was analyzed by electrophoresis on a 1% agarose gel to determine which reactions were successful in extending the sequence.

[0447] The extended nucleotides were desalted and concentrated, transferred to 384-well plates, digested with CviJI cholera virus endonuclease (Molecular Biology Research, Madison Wis.), and sonicated or sheared prior to religation into pUC 18 vector (Amersham Pharmacia Biotech). For shotgun sequencing, the digested nucleotides were separated on low concentration (0.6 to 0.8%) agarose gels, fragments were excised, and agar digested with Agar ACE (Promega). Extended clones were religated using T4 ligase (New England Biolabs, Beverly Mass.) into pUC 18 vector (Amersham Pharmacia Biotech), treated with Pfu DNA polymerase (Stratagene) to fill-in restriction site overhangs, and transfected into competent E. coli cells. Transformed cells were selected on antibiotic-containing media, and individual colonies were picked and cultured overnight at 37° C. in 384-well plates in LB/2× carb liquid media.

[0448] The cells were lysed, and DNA was amplified by PCR using Taq DNA polymerase (Amersham Pharmacia Biotech) and Pfu DNA polymerase (Stratagene) with the following parameters: Step 1: 94° C., 3 min; Step 2: 94° C., 15 sec; Step 3: 60° C., 1 min; Step 4: 72° C., 2 min; Step 5: steps 2, 3, and 4 repeated 29 times; Step 6: 72° C., 5 min; Step 7: storage at 4° C. DNA was quantified by PICOGREEN reagent (Molecular Probes) as described above. Samples with low DNA recoveries were reamplified using the same conditions as described above. Samples were diluted with 20% dimethysulfoxide (1:2, v/v), and sequenced using DYENAMIC energy transfer sequencing primers and the DYENAMIC DIRECT kit (Amersham Pharmacia Biotech) or the ABI PRISM BIGDYE Terminator cycle sequencing ready reaction kit (Applied Biosystems).

[0449] In like manner, full length polynucleotide sequences are verified using the above procedure or are used to obtain 5′ regulatory sequences using the above procedure along with oligonucleotides designed for such extension, and an appropriate genomic library.

[0450] IX. Identification of Single Nucleotide Polymorphisms in CGDD Encoding Polynucleotides

[0451] Common DNA sequence variants known as single nucleotide polymorphisms (SNPs) were identified in SEQ ID NO:22-42 using the LIFESEQ database (Incyte Genomics). Sequences from the same gene were clustered together and assembled as described in Example m, allowing the identification of all sequence variants in the gene. An algorithm consisting of a series of filters was used to distinguish SNPs from other sequence variants. Preliminary filters removed the majority of basecall errors by requiring a minimum Phred quality score of 15, and removed sequence alignment errors and errors resulting from improper trimming of vector sequences, chimeras, and splice variants. An automated procedure of advanced chromosome analysis analysed the original chromatogram files in the vicinity of the putative SNP. Clone error filters used statistically generated algorithms to identify errors introduced during laboratory processing, such as those caused by reverse transcriptase, polymerase, or somatic mutation. Clustering error filters used statistically generated algorithms to identify errors resulting from clustering of close homologs or pseudogenes, or due to contamination by non-human sequences. A final set of filters removed duplicates and SNPs found in immunoglobulins or T-cell receptors.

[0452] Certain SNPs were selected for further characterization by mass spectrometry using the high throughput MASSARRAY system (Sequenom, Inc.) to analyze allele frequencies at the SNP sites in four different human populations. The Caucasian population comprised 92 individuals (46 male, 46 female), including 83 from Utah, four French, three Venezualan, and two Amish individuals. The African population comprised 194 individuals (97 male, 97 female), all African Americans. The Hispanic population comprised 324 individuals (162 male, 162 female), all Mexican Hispanic. The Asian population comprised 126 individuals (64 male, 62 female) with a reported parental breakdown of 43% Chinese, 31% Japanese, 13% Korean, 5% Vietnamese, and 8% other Asian. Allele frequencies were first analyzed in the Caucasian population; in some cases those SNPs which showed no allelic variance in this population were not further tested in the other three populations.

[0453] X. Labeling and Use of Individual Hybridization Probes

[0454] Hybridization probes derived from SEQ ID NO:22-42 are employed to screen cDNAs, genomic DNAs, or mRNAs. Although the labeling of oligonucleotides, consisting of about 20 base pairs, is specifically described, essentially the same procedure is used with larger nucleotide fragments. Oligonucleotides are designed using state-of-the-art software such as OLIGO 4.06 software (National Biosciences) and labeled by combining 50 pmol of each oligomer, 250 μCi of [γ-³²P] adenosine triphosphate (Amersham Pharmacia Biotech), and T4 polynucleotide kinase (DuPont NEN, Boston Mass.). The labeled oligonucleotides are substantially purified using a SEPHADEX G-25 superfine size exclusion dextran bead column (Amersham Pharmacia Biotech). An aliquot containing 107 counts per minute of the labeled probe is used in a typical membrane-based hybridization analysis of human genomic DNA digested with one of the following endonucleases: Ase I, Bgl II, Eco RI, Pst I, Xba I, or Pvu II (DuPont NEN).

[0455] The DNA from each digest is fractionated on a 0.7% agarose gel and transferred to nylon membranes (Nytran Plus, Schleicher & Schuell, Durham N.H.). Hybridization is carried out for 16 hours at 40° C. To remove nonspecific signals, blots are sequentially washed at room temperature under conditions of up to, for example, 0.1×saline sodium citrate and 0.5% sodium dodecyl sulfate. Hybridization patterns are visualized using autoradiography or an alternative imaging means and compared.

[0456] XI. Microarrays

[0457] The linkage or synthesis of array elements upon a microarray can be achieved utilizing photolithography, piezoelectric printing (ink-jet printing, See, e.g., Baldeschweiler, supra.), mechanical microspotting technologies, and derivatives thereof. The substrate in each of the aforementioned technologies should be uniform and solid with a non-porous surface (Schena (1999), supra). Suggested substrates include silicon, silica, glass slides, glass chips, and silicon wafers. Alternatively, a procedure analogous to a dot or slot blot may also be used to arrange and link elements to the surface of a substrate using thermal, UV, chemical, or mechanical bonding procedures. A typical array may be produced using available methods and machines well known to those of ordinary skill in the art and may contain any appropriate number of elements. (See, e.g., Schena, M. et al. (1995) Science 270:467-470; Shalon, D. et al. (1996) Genome Res. 6:639-645; Marshall, A. and J. Hodgson (1998) Nat. Biotechnol. 16:27-31.)

[0458] Full length cDNAs, Expressed Sequence Tags (ESTs), or fragments or oligomers thereof may comprise the elements of the microarray. Fragments or oligomers suitable for hybridization can be selected using software well known in the art such as LASERGENE software (DNASTAR). The array elements are hybridized with polynucleotides in a biological sample. The polynucleotides in the biological sample are conjugated to a fluorescent label or other molecular tag for ease of detection. After hybridization, nonhybridized nucleotides from the biological sample are removed, and a fluorescence scanner is used to detect hybridization at each array element. Alternatively, laser desorbtion and mass spectrometry may be used for detection of hybridization. The degree of complementarity and the relative abundance of each polynucleotide which hybridizes to an element on the microarray may be assessed. In one embodiment, microarray preparation and usage is described in detail below.

[0459] Tissue or Cell Sample Preparation

[0460] Total RNA is isolated from tissue samples using the guanidinium thiocyanate method and poly(A)⁺ RNA is purified using the oligo-(dT) cellulose method. Each poly(A)⁺ RNA sample is reverse transcribed using MMLV reverse-transcriptase, 0.05 pg/μl oligo-(dT) primer (21mer), 1× first strand buffer, 0.03 units/μl RNase inhibitor, 500 μM dATP, 500 μM dGTP, 500 μM dTTP, 40 μM dCTP, 40 μM dCTP-Cy3 (BDS) or dCTP-Cy5 (Amersham Pharmacia Biotech). The reverse transcription reaction is performed in a 25 ml volume containing 200 ng poly(A)⁺ RNA with GEMBRIGHT kits (Incyte). Specific control poly(A)⁺ RNAs are synthesized by in vitro transcription from non-coding yeast genomic DNA. After incubation at 37° C. for 2 hr, each reaction sample (one with Cy3 and another with Cy5 labeling) is treated with 2.5 ml of 0.5M sodium hydroxide and incubated for 20 minutes at 85° C. to the stop the reaction and degrade the RNA. Samples are purified using two successive CHROMA SPIN 30 gel filtration spin columns (CLONTECH Laboratories, Inc. (CLONTECH), Palo Alto Calif.) and after combining, both reaction samples are ethanol precipitated using 1 ml of glycogen (1 mg/ml), 60 ml sodium acetate, and 300 ml of 100% ethanol. The sample is then dried to completion using a SpeedVAC (Savant Instruments Inc., Holbrook N.Y.) and resuspended in 14 μl 5×SSC/0.2% SDS.

[0461] Microarray Preparation

[0462] Sequences of the present invention are used to generate array elements. Each array element is amplified from bacterial cells containing vectors with cloned cDNA inserts. PCR amplification uses primers complementary to the vector sequences flanking the cDNA insert. Array elements are amplified in thirty cycles of PCR from an initial quantity of 1-2 ng to a final quantity greater than 5 μg. Amplified array elements are then purified using SEPHACRYL-400 (Amersham Pharmacia Biotech).

[0463] Purified array elements are immobilized on polymer-coated glass slides. Glass microscope slides (Corning) are cleaned by ultrasound in 0.1% SDS and acetone, with extensive distilled water washes between and after treatments. Glass slides are etched in 4% hydrofluoric acid (VWR Scientific Products Corporation (VWR), West Chester Pa.), washed extensively in distilled water, and coated with 0.05% aminopropyl silane (Sigma) in 95% ethanol. Coated slides are cured in a 110° C. oven.

[0464] Array elements are applied to the coated glass substrate using a procedure described in U.S. Pat. No. 5,807,522, incorporated herein by reference. 1 μl of the array element DNA, at an average concentration of 100 ng/μl, is loaded into the open capillary printing element by a high-speed robotic apparatus. The apparatus then deposits about 5 nl of array element sample per slide.

[0465] Microarrays are UV-crosslinked using a STRATALINKER UV-crosslinker (Stratagene). Microarrays are washed at room temperature once in 0.2% SDS and three times in distilled water. Non-specific binding sites are blocked by incubation of microarrays in 0.2% casein in phosphate buffered saline (PBS) (Tropix, Inc., Bedford Mass.) for 30 minutes at 60° C. followed by washes in 0.2% SDS and distilled water as before.

[0466] Hybridization

[0467] Hybridization reactions contain 9 μl of sample mixture consisting of 0.2 μg each of Cy3 and Cy5 labeled cDNA synthesis products in 5×SSC, 0.2% SDS hybridization buffer. The sample mixture is heated to 65° C. for 5 minutes and is aliquoted onto the microarray surface and covered with an 1.8 cm² coverslip. The arrays are transferred to a waterproof chamber having a cavity just slightly larger than a microscope slide. The chamber is kept at 100% humidity internally by the addition of 140 μl of 5×SSC in a corner of the chamber. The chamber containing the arrays is incubated for about 6.5 hours at 60° C. The arrays are washed for 10 min at 45° C. in a first wash buffer (1×SSC, 0.1% SDS), three times for 10 minutes each at 45° C. in a second wash buffer (0.1×SSC), and dried.

[0468] Detection

[0469] Reporter-labeled hybridization complexes are detected with a microscope equipped with an Innova 70 mixed gas 10 W laser (Coherent, Inc., Santa Clara Calif.) capable of generating spectral lines at 488 nm for excitation of Cy3 and at 632 nm for excitation of Cy5. The excitation laser light is focused on the array using a 20× microscope objective (Nikon, Inc., Melville N.Y.). The slide containing the array is placed on a computer-controlled X-Y stage on the microscope and raster-scanned past the objective. The 1.8 cm×1.8 cm array used in the present example is scanned with a resolution of 20 micrometers.

[0470] In two separate scans, a mixed gas multiline laser excites the two fluorophores sequentially. Emitted light is split, based on wavelength, into two photomultiplier tube detectors (PMT R1477, Hamamatsu Photonics Systems, Bridgewater N.J.) corresponding to the two fluorophores. Appropriate filters positioned between the array and the photomultiplier tubes are used to filter the signals. The emission maxima of the fluorophores used are 565 nm for Cy3 and 650 nm for Cy5. Each array is typically scanned twice, one scan per fluorophore using the appropriate filters at the laser source, although the apparatus is capable of recording the spectra from both fluorophores simultaneously.

[0471] The sensitivity of the scans is typically calibrated using the signal intensity generated by a cDNA control species added to the sample mixture at a known concentration. A specific location on the array contains a complementary DNA sequence, allowing the intensity of the signal at that location to be correlated with a weight ratio of hybridizing species of 1:100,000. When two samples from different sources (e.g., representing test and control cells), each labeled with a different fluorophore, are hybridized to a single array for the purpose of identifying genes that are differentially expressed, the calibration is done by labeling samples of the calibrating cDNA with the two fluorophores and adding identical amounts of each to the hybridization mixture.

[0472] The output of the photomultiplier tube is digitized using a 12-bit RTI-835H analog-to-digital (A/D) conversion board (Analog Devices, Inc., Norwood Mass.) installed in an IBM-compatible PC computer. The digitized data are displayed as an image where the signal intensity is mapped using a linear 20-color transformation to a pseudocolor scale ranging from blue (low signal) to red (high signal). The data is also analyzed quantitatively. Where two different fluorophores are excited and measured simultaneously, the data are first corrected for optical crosstalk (due to overlapping emission spectra) between the fluorophores using each fluorophore's emission spectrum.

[0473] A grid is superimposed over the fluorescence signal image such that the signal from each spot is centered in each element of the grid. The fluorescence signal within each element is then integrated to obtain a numerical value corresponding to the average intensity of the signal. The software used for signal analysis is the GEMTOOLS gene expression analysis program (Incyte).

[0474] Expression

[0475] Normal breast cell lines are obtained as follows. Primary mammary gland cells are isolated from a donor with fibrocystic breast disease. Alternatively, primary breast epithelial cells are isolated from a normal donor. Breast carcinoma cells are derived in vitro from cells emigrating from a tumor. Normal and various stages of tumorigenic breast cell lines were purchased from American Type Culture Collection (ATCC), (Manassas, Va.).

[0476] For example, SEQ ID NO:34 showed differential expression in cancer cell lines or tumorous tissue versus non-cancerous cell lines or tissues as determined by microarray analysis. The expression of CGDD-13 was increased by at least three fold in a breast tumor cell line that was harvested from a donor with an early stage of tumor progression.

[0477] In an alternative example, SEQ ID NO:37 showed differential expression in inflammatory responses as determined by microarray analysis. The expression of SEQ ID NO:37 was increased by at least two fold in PBMCs treated with LPS relative to untreated PBMCs. Therefore, SEQ ID NO:37 is useful in diagnostic assays for inflammatory responses.

[0478] In addition, SEQ ID NO:37 showed differential expression in non-malignant mammary epithelial cells versus various breast carcinoma lines as determined by microarray analysis. The expression of SEQ ID NO:37 was decreased by at least two fold in the breast carcinoma lines relative to non-malignant mammary epithelial cells. Therefore, SEQ ID NO:37 is useful in diagnostic assays for detection of breast cancer.

[0479] In an alternative example, SEQ ID NO:41 showed differential expression in brain cingulate from a patient with Alzheimer's disease compared to matched microscopically normal tissue from the same donor as determined by microarray analysis. The expression of CGDD-19 was increased in cingulate tissue with Alzheimer's disease. Therefore, SEQ ID NO:41 is useful in diagnostic assays for neurological disorders, particularly Alzheimer's disease.

[0480] XII. Complementary Polynucleotides

[0481] Sequences complementary to the CGDD-encoding sequences, or any parts thereof, are used to detect, decrease, or inhibit expression of naturally occurring CGDD. Although use of oligonucleotides comprising from about 15 to 30 base pairs is described, essentially the same procedure is used with smaller or with larger sequence fragments. Appropriate oligonucleotides are designed using OLIGO 4.06 software (National Biosciences) and the coding sequence of CGDD. To inhibit transcription, a complementary oligonucleotide is designed from the most unique 5′ sequence and used to prevent promoter binding to the coding sequence. To inhibit translation, a complementary oligonucleotide is designed to prevent ribosomal binding to the CGDD-encoding transcript.

[0482] XIII. Expression of CGDD

[0483] Expression and purification of CGDD is achieved using bacterial or virus-based expression systems. For expression of CGDD in bacteria, cDNA is subcloned into an appropriate vector containing an antibiotic resistance gene and an inducible promoter that directs high levels of cDNA transcription. Examples of such promoters include, but are not limited to, the trp-lac (tac) hybrid promoter and the T5 or T7 bacteriophage promoter in conjunction with the lac operator regulatory element. Recombinant vectors are transformed into suitable bacterial hosts, e.g., BL21(DE3). Antibiotic resistant bacteria express CGDD upon induction with isopropyl beta-D-thiogalactopyranoside (IPTG). Expression of CGDD in eukaryotic cells is achieved by infecting insect or mammalian cell lines with recombinant Autographica californica nuclear polyhedrosis virus (AcMNPV), commonly known as baculovirus. The nonessential polyhedrin gene of baculovirus is replaced with cDNA encoding CGDD by either homologous recombination or bacterial-mediated transposition involving transfer plasmid intermediates. Viral infectivity is maintained and the strong polyhedrin promoter drives high levels of cDNA transcription. Recombinant baculovirus is used to infect Spodoptera frugiperda (Sf9) insect cells in most cases, or human hepatocytes, in some cases. Infection of the latter requires additional genetic modifications to baculovirus. (See Engelhard, E. K. et al. (1994) Proc. Natl. Acad. Sci. USA 91:3224-3227; Sandig, V. et al. (1996) Hum. Gene Ther. 7:1937-1945.)

[0484] In most expression systems, CGDD is synthesized as a fusion protein with, e.g., glutathione S-transferase (GST) or a peptide epitope tag, such as FLAG or 6-His, permitting rapid, single-step, affinity-based purification of recombinant fusion protein from crude cell lysates. GST, a 26-kilodalton enzyme from Schistosoma japonicum, enables the purification of fusion proteins on immobilized glutathione under conditions that maintain protein activity and antigenicity (Amersham Pharmacia Biotech). Following purification, the GST moiety can be proteolytically cleaved from CGDD at specifically engineered sites. FLAG, an 8-amino acid peptide, enables immunoaffinity purification using commercially available monoclonal and polyclonal anti-FLAG antibodies (Eastman Kodak). 6-His, a stretch of six consecutive histidine residues, enables purification on metal-chelate resins (QIAGEN). Methods for protein expression and purification are discussed in Ausubel (1995, supra, ch. 10 and 16). Purified CGDD obtained by these methods can be used directly in the assays shown in Examples XVII, XVIII, and XIX, where applicable.

[0485] XIV. Functional Assays

[0486] CGDD function is assessed by expressing the sequences encoding CGDD at physiologically elevated levels in mammalian cell culture systems. cDNA is subcloned into a mammalian expression vector containing a strong promoter that drives high levels of cDNA expression. Vectors of choice include PCMV SPORT (Life Technologies) and PCR3.1 (Invitrogen, Carlsbad Calif.), both of which contain the cytomegalovirus promoter. 5-10 μg of recombinant vector are transiently transfected into a human cell line, for example, an endothelial or hematopoietic cell line, using either liposome formulations or electroporation. 1-2 μg of an additional plasmid containing sequences encoding a marker protein are co-transfected. Expression of a marker protein provides a means to distinguish transfected cells from nontransfected cells and is a reliable predictor of cDNA expression from the recombinant vector. Marker proteins of choice include, e.g., Green Fluorescent Protein (GFP; Clontech), CD64, or a CD64-GFP fusion protein. Flow cytometry (FCM), an automated, laser optics-based technique, is used to identify transfected cells expressing GFP or CD64-GFP and to evaluate the apoptotic state of the cells and other cellular properties. FCM detects and quantifies the uptake of fluorescent molecules that diagnose events preceding or coincident with cell death. These events include changes in nuclear DNA content as measured by staining of DNA with propidium iodide; changes in cell size and granularity as measured by forward light scatter and 90 degree side light scatter; down-regulation of DNA synthesis as measured by decrease in bromodeoxyuridine uptake; alterations in expression of cell surface and intracellular proteins as measured by reactivity with specific antibodies; and alterations in plasma membrane composition as measured by the binding of fluorescein-conjugated Annexin V protein to the cell surface. Methods in flow cytometry are discussed in Ormerod, M. G. (1994) Flow Cytometry, Oxford, New York N.Y.

[0487] The influence of CGDD on gene expression can be assessed using highly purified populations of cells transfected with sequences encoding CGDD and either CD64 or CD64-GFP. CD64 and CD64-GFP are expressed on the surface of transfected cells and bind to conserved regions of human immunoglobulin G (IgG). Transfected cells are efficiently separated from nontransfected cells using magnetic beads coated with either human IgG or antibody against CD64 (DYNAL, Lake Success N.Y.). mRNA can be purified from the cells using methods well known by those of skill in the art. Expression of mRNA encoding CGDD and other genes of interest can be analyzed by northern analysis or microarray techniques.

[0488] XV. Production of CGDD Specific Antibodies

[0489] CGDD substantially purified using polyacrylamide gel electrophoresis (PAGE; see, e.g., Harrington, M. G. (1990) Methods Enzymol. 182:488-495), or other purification techniques, is used to immunize animals (e.g., rabbits, mice, etc.) and to produce antibodies using standard protocols.

[0490] Alternatively, the CGDD amino acid sequence is analyzed using LASERGENE software (DNASTAR) to determine regions of high immunogenicity, and a corresponding oligopeptide is synthesized and used to raise antibodies by means known to those of skill in the art. Methods for selection of appropriate epitopes, such as those near the C-terminus or in hydrophilic regions are well described in the art. (See, e.g., Ausubel, 1995, supra, ch. 11.)

[0491] Typically, oligopeptides of about 15 residues in length are synthesized using an ABI 431A peptide synthesizer (Applied Biosystems) using FMOC chemistry and coupled to KLH (Sigma-Aldrich, St. Louis Mo.) by reaction with N-maleimidobenzoyl-N-hydroxysuccinimide ester (MBS) to increase immunogenicity. (See, e.g., Ausubel, 1995, supra.) Rabbits are immunized with the oligopeptide-KLH complex in complete Freund's adjuvant. Resulting antisera are tested for antipeptide and anti-CGDD activity by, for example, binding the peptide or CGDD to a substrate, blocking with 1% BSA, reacting with rabbit antisera, washing, and reacting with radio-iodinated goat anti-rabbit IgG.

[0492] XVI. Purification of Naturally Occurring CGDD Using Specific Antibodies

[0493] Naturally occurring or recombinant CGDD is substantially purified by immunoaffinity chromatography using antibodies specific for CGDD. An immunoaffinity column is constructed by covalently coupling anti-CGDD antibody to an activated chromatographic resin, such as CNBr-activated SEPHAROSE (Amersham Pharmacia Biotech). After the coupling, the resin is blocked and washed according to the manufacturer's instructions.

[0494] Media containing CGDD are passed over the immunoaffinity column, and the column is washed under conditions that allow the preferential absorbance of CGDD (e.g., high ionic strength buffers in the presence of detergent). The column is eluted under conditions that disrupt antibody/CGDD binding (e.g., a buffer of pH 2 to pH 3, or a high concentration of a chaotrope, such as urea or thiocyanate ion), and CGDD is collected.

[0495] XVII. Identification of Molecules Which Interact with CGDD

[0496] CGDD, or biologically active fragments thereof, are labeled with ¹²⁵I Bolton-Hunter reagent. (See, e.g., Bolton, A. E. and W. M. Hunter (1973) Biochem. J. 133:529-539.) Candidate molecules previously arrayed in the wells of a multi-well plate are incubated with the labeled CGDD, washed, and any wells with labeled CGDD complex are assayed. Data obtained using different concentrations of CGDD are used to calculate values for the number, affinity, and association of CGDD with the candidate molecules.

[0497] Alternatively, molecules interacting with CGDD are analyzed using the yeast two-hybrid system as described in Fields, S. and O. Song (1989) Nature 340:245-246, or using commercially available kits based on the two-hybrid system, such as the MATCHMAKER system (Clontech).

[0498] CGDD may also be used in the PATHCALLING process (CuraGen Corp., New Haven Conn.) which employs the yeast two-hybrid system in a high-throughput manner to determine all interactions between the proteins encoded by two large libraries of genes (Nandabalan, K. et al. (2000) U.S. Pat. No. 6,057,101).

[0499] XVIII. Demonstration of CGDD Activity

[0500] CGDD activity is demonstrated by measuring the induction of terminal differentiation or cell cycle progression when CGDD is expressed at physiologically elevated levels in mammalian cell culture systems. cDNA is subcloned into a mammalian expression vector containing a strong promoter that drives high levels of cDNA expression. Vectors of choice include PCMV SPORT (Life Technologies, Gaithersburg, Md.) and PCR 3.1 (Invitrogen, Carlsbad, Calif.), both of which contain the cytomegalovirus promoter. 5-10 μg of recombinant vector are transiently transfected into a human cell line, preferably of endothelial or hematopoietic origin, using either liposome formulations or electroporation. 1-2 μg of an additional plasmid containing sequences encoding a marker protein are co-transfected. Expression of a marker protein provides a means to distinguish transfected cells from nontransfected cells and is a reliable predictor of cDNA expression from the recombinant vector. Marker proteins of choice include, e.g., Green Fluorescent Protein (GFP) (Clontech, Palo Alto, Calif.), CD64, or a CD64-GFP fusion protein. Flow cytometry detects and quantifies the uptake of fluorescent molecules that diagnose events preceding or coincident with cell cycle progression or terminal differentiation. These events include changes in nuclear DNA content as measured by staining of DNA with propidium iodide; changes in cell size and granularity as measured by forward light scatter and 90 degree side light scatter; up or down-regulation of DNA synthesis as measured by decrease in bromodeoxyuridine uptake; alterations in expression of cell surface and intracellular proteins as measured by reactivity with specific antibodies; and alterations in plasma membrane composition as measured by the binding of fluorescein-conjugated Annexin V protein to the cell surface. Methods in flow cytometry are discussed in Ormerod, M. G. (1994) Flow Cytometry, Oxford, New York, N.Y.

[0501] Alternatively, an in vitro assay for CGDD activity measures the transformation of normal human fibroblast cells overexpressing antisense CGDD RNA (Garkavtsev, I. and Riabowol, K. (1997) Mol. Cell Biol. 17:2014-2019). cDNA encoding CGDD is subcloned into the pLNCX retroviral vector to enable expression of antisense CGDD RNA. The resulting construct is transfected into the ecotropic BOSC23 virus-packaging cell line. Virus contained in the BOSC23 culture supernatant is used to infect the amphotropic CAKS virus-packaging cell line. Virus contained in the CAK8 culture supernatant is used to infect normal human fibroblast (Hs68) cells. Infected cells are assessed for the following quantifiable properties characteristic of transformed cells: growth in culture to high density associated with loss of contact inhibition, growth in suspension or in soft agar, formation of colonies or foci, lowered serum requirements, and ability to induce tumors when injected into immunodeficient mice. The activity of CGDD is proportional to the extent of transformation of Hs68 cells.

[0502] Alternatively, CGDD can be expressed in a mammalian cell line by transforming the cells with a eukaryotic expression vector encoding CGDD. Eukaryotic expression vectors are commercially available, and the techniques to introduce them into cells are well known to those skilled in the art. To assay the cellular localization of CGDD, cells are fractionated as described by Jiang H. P. et al. (1992; Proc. Natl. Acad. Sci. 89: 7856-7860). Briefly, cells pelleted by low-speed centrifugation are resuspended in buffer (10 mM TRIS-HCl, pH 7.4/10 mM NaCl/3 mM MgCl₂/5 mM EDTA with 10 ug/ml aprotinin, 10 ug/ml leupeptin, 10 ug/ml pepstatin A, 0.2 mM phenylmethylsulfonyl fluoride) and homogenized. The homogenate is centrifuged at 600×g for 5 minutes. The particulate and cytosol fractions are separated by ultracentrifugation of the supernatant at 100,000×g for 60 minutes. The nuclear fraction is obtained by resuspending the 600×g pellet in sucrose solution (0.25 M sucrose/10 mM TRIS-HCl, pH 7.4/2 mM MgCl₂) and recentrifuged at 600×g. Equal amounts of protein from each fraction are applied to an SDS/10% polyacrylamide gel and blotted onto membranes. Western blot analysis is performed using CGDD anti-serum. The localization of CGDD is assessed by the intensity of the corresponding band in the nuclear fraction relative to the intensity in the other fractions. Alternatively, the presence of CGDD in cellular fractions is examined by fluorescence microscopy using a fluorescent antibody specific for CGDD.

[0503] Alternatively, CGDD activity may be demonstrated as the ability to interact with its associated Ras superfamily protein, in an in vitro binding assay. The candidate Ras superfamily proteins are expressed as fusion proteins with glutathione S-transferase (GST), and purified by affinity chromatography on glutathione-Sepharose. The Ras superfamily proteins are loaded with GDP by incubating 20 nM Tris buffer, pH 8.0, containing 100 mM NaCl, 2 mM EDTA, 5 mM MgCl2, 0.2 mM DTT, 100 μM AMP-PNP and 10 μM GDP at 30° C. for 20 minutes. CGDD is expressed as a FLAG fusion protein in a baculovirus system. Extracts of these baculovirus cells containing CGDD-FLAG fusion proteins are precleared with GST beads, then incubated with GST-Ras superfamily fusion proteins. The complexes formed are precipitated by glutathione-Sepharose and separated by SDS-polyacrylamide gel electrophoresis. The separated proteins are blotted onto nitrocellulose membranes and probed with commercially available anti-FLAG antibodies. CGDD activity is proportional to the amount of CGDD-FLAG fusion protein detected in the complex.

[0504] Alternatively, as demonstrated by Li and Cohen (Li, L. and S. N. Cohen (1995) Cell 85:319-329), the ability of CGDD to suppress tumorigenesis can be measured by designing an antisense sequence to the 5′ end of the gene and transfecting NIH 3T3 cells with a vector transcribing this sequence. The suppression of the endogenous gene will allow transformed fibroblasts to produce clumps of cells capable of forming metastatic tumors when introduced into nude mice.

[0505] Alternatively, an assay for CGDD activity measures the effect of injected CGDD on the degradation of maternal transcripts. Procedures for oocyte collection from Swiss albino mice, injection, and culture are as described in Stutz (supra). A decrease in the degradation of maternal RNAs as compared to control oocytes is indicative of CGDD activity. In the alternative, CGDD activity is measured as the ability of purified CGDD to bind to RNAse as measured by the assays described in Example XVII.

[0506] Alternatively, an assay for CGDD activity measures syncytium formation in COS cells transfected with an CGDD expression plasmid, using the two-component fusion assay described in Mi (supra). This assay takes advantage of the fact that human interleukin. 12 (IL-12) is a heterodimer comprising subunits with molecular weights of 35 kD (p35) and 40 kD (p40). COS cells transfected with expression plasmids carrying the gene for p35 are mixed with COS cells cotransfected with expression plasmids carrying the genes for p40 and CGDD. The level of IL-12 activity in the resulting conditioned medium corresponds to the activity of CGDD in this assay. Syncytium formation may also be measured by light microscopy (Mi et al. supra).

[0507] An alternative assay for CGDD activity measures cell proliferation as the amount of newly initiated DNA synthesis in Swiss mouse 3T3 cells. A plasmid containing polynucleotides encoding CGDD is transfected into quiescent 3T3 cultured cells using methods well known in the art. The transiently transfected cells are then incubated in the presence of [³H]thymidine or a radioactive DNA precursor such as [α³²P]ATP. Where applicable, varying amounts of CGDD ligand are added to the transfected cells. Incorporation of [³H]thymidine into acid-precipitable DNA is measured over an appropriate time interval, and the amount incorporated is directly proportional to the amount of newly synthesized DNA and CGDD activity.

[0508] Alternatively, CGDD activity is measured by the cyclin-ubiquitin ligation assay (Townsley, F. M. et al. (1997) Proc. Natl. Acad. Sci. USA 94:2362-2367). The reaction contains in a volume of 10 μl, 40 mM Tris.HCl (pH 7.6), 5 mM Mg Cl₂, 0.5 mM ATP, 10 mM phosphocreatine, 50 μg of creatine phosphokinase/ml, 1 mg reduced carboxymethylated bovine serum albumin/ml, 50 μM ubiquitin, 1 μM ubiquitin aldehyde, 1-2 pmol ¹²⁵I-labeled cyclin B, 1 pmol E1, 1 μM okadaic acid, 10 μg of protein of M-phase fraction 1A (containing active E3-C and essentially free of E2-C), and varying amounts of CGDD. The reaction is incubated at 18° C. for 60 minutes. Samples are then separated by electrophoresis on an SDS polyacrylamide gel. The amount of ¹²⁵I-cyclin-ubiquitin formed is quantified by PHOSPHORIMAGER analysis. The amount of cyclin-ubiquitin formation is proportional to the activity of CGDD in the reaction.

[0509] Alternatively, an assay for CGDD activity uses radiolabeled nucleotides, such as [α³²P]ATP, to measure either the incorporation of radiolabel into DNA during DNA synthesis, or fragmentation of DNA that accompanies apoptosis. Mammalian cells are transfected with plasmid containing cDNA encoding CGDD by methods well known in the art. Cells are then incubated with radiolabeled nucleotide for various lengths of time. Chromosomal DNA is collected, and radioactivity is detected using a scintillation counter. Incorporation of radiolabel into chromosomal DNA is proportional to the degree of stimulation of the cell cycle. To determine if CGDD promotes apoptosis, chromosomal DNA is collected as above, and analyzed using polyacrylamide gel electrophoresis, by methods well known in the art. Fragmentation of DNA is quantified by comparison to untransfected control cells, and is proportional to the apoptotic activity of CGDD.

[0510] Alternatively, cyclophilin activity of CGDD is measured using a chymotrypsin-coupled assay to measure the rate of cis to trans interconversion (Fischer, G., Bang, H., and Mech, C. (1984) Biomed. Biochim. Acta 43: 1101-1111). The chymotrypsin is used to estimate the trans-substrate cleavage activity at Xaa-Pro peptide bonds, wherein the rate constant for the cis to trans isomerization can be obtained by measuring the rate constant of the substrate hydrolysis at the slow phase. Samples are incubated in the presence or absence of the immunosuppressant drugs CsA or FK506, reactions initiated by addition of chymotrypsin, and the fluorescent reaction measured. The enzymatic rate constant is calculated from the equation k_(app)=k_(H2O+k) _(enz), wherein first order kinetics are displayed, and where one unit of PPIase activity is defined as k_(enz) (s⁻¹).

[0511] A fluorescence monitoring assay for detecting activated Ras using RRP22 is as follows. The RRP22 binding domain (RRP22BD) of c-Raf1 (a kinase activated during reentry into meiosis) is synthesized from two unprotected peptide segments by native chemical ligation. Two fluorescent amino acids with structures based on the nitrobenz-2-oxa-1,3-diazole and coumaryl chromophores are incorporated close to the RRP22BD/RRP22-GTP binding surface followed by introduction of a C-terminal tag consisting of His(6). The K_(D) values for binding of the site-specifically modified proteins to Ras-GTP are compared to that of wild-type RBD. Ras-GTP is detected within the 100 nM range by immobilization of C-terminal His(6) tag-modified fluorescent RBD onto Ni-NTA-coated surfaces. Ras-GDP does not bind to the immobilized RBD, thus allowing discrimination between inactive and activated Ras (Becker, C. F. (2001) Chem. Biol. 8:243-252).

[0512] CGDD is assayed for Ras binding by the method of Vavvas et al. (supra). CGDD is expressed as a GST fusion protein and the GST-CGDD fusion is incubated with Ras in the presence of either GTPγS or GDPβS. Glutathione-SEPHAROSE beads (APB) are added to recover the GST-CGDD fusion and GST-CGDD-Ras complexes from solution. Proteins are eluted from the glutathione-SEPHAROSE beads with SDS sample buffer and separated by SDS-PAGE. Following electrophoresis, proteins are transferred to a PVDF membrane (APB) and probed for Ras with monoclonal anti-Ras antibodies.

[0513] Regulation of Wnt5a by cell-to-cell contacts is shown by adding various metabolic agents that selectively block protein tyrosine kinases (genistein) or cytochalasin D to HB2, a normal breast epithelial cell line. Cytoskeleton reorganization following cytochalasin D treatment causes an induction of Wnt5a, which is associated with changes in cell morphology. Cancer cell lines treated with cytochalasin D show no changes in cell morphology nor Wnt5a induction (Jonsson, M. et al. (1998) Br. J. Cancer 78:430-438).

[0514] XIX. CGDD Binding Assays

[0515] A quantitative immunoassay for the CGDD cyclophilin measures its affinity for stereospecific binding to the immunosuppressant drug cyclosporin (Quesniaux, V. F., et al. (1987) Eur. J. Immunol. 17: 1359-1365). In this assay, the cyclophilin-cyclosporin complex is coated on a solid phase, with binding detected using anti-cyclophilin rabbit antiserum enhanced by an antiglobulin-enzyme conjugate. Complexing of the CGDD immunophilin, cyclophilin, with the immunosuppressant drug cyclosporin at critical residues facilitates immunosuppressant activity, such as that which occurs during tumorigeneis.

[0516] A binding assay developed to measure the non-covalent binding between FKBPs and immunosuppressant drugs in the gas phase utilizes electrospray ionization mass spectrometry (Trepanier, D. J., et al. (1999) Ther. Drug Monit. 21: 274-280). In electrospray ionization, ions are generated by creating a fine spray of highly charged droplets in the presence of a strong electric field; as the droplet decreases in size, the charge density on the surface increases. Ions are electrostatically directed into a mass analyzer, where ions of opposite charge are generated in spatially separate sources and then swept into capillary inlets where the flows are merged and where reactions occur. By comparing the charge states of bound versus unbound FKBP/immunosuppressive drug complexes, relative binding affinities can be established and correlated with in vitro binding and immunosuppressive activity.

[0517] Various modifications and variations of the described methods and systems of the invention will be apparent to those skilled in the art without departing from the scope and spirit of the invention. Although the invention has been described in connection with certain embodiments, it should be understood that the invention as claimed should not be unduly limited to such specific embodiments. Indeed, various modifications of the described modes for carrying out the invention which are obvious to those skilled in molecular biology or related fields are intended to be within the scope of the following claims. TABLE 1 Incyte Incyte Incyte Project Polypeptide Polypeptide Polynucleotide Polynucleotide CA2 ID SEQ ID NO: ID SEQ ID NO: ID Reagents 1351608 1 1351608CD1 22 1351608CB1 4259314 2 4259314CD1 23 4259314CB1 2747431CA2, 3421573CA2 3660046 3 3660046CD1 24 3660046CB1 3016416 4 3016416CD1 25 3016416CB1 7291179CA2 2133755 5 2133755CD1 26 2133755CB1 90067312CA2 5259957 6 5259957CD1 27 5259957CB1 5259957CA2 55029783 7 55029783CD1 28 55029783CB1 4949559CA2 8032202 8 8032202CD1 29 8032202CB1 6937367 9 6937367CD1 30 6937367CB1 3876510 10 3876510CD1 31 3876510CB1 4900076 11 4900076CD1 32 4900076CB1 1543848 12 1543848CD1 33 1543848CB1 6254070 13 6254070CD1 34 6254070CB1 7677372CA2, 90072067CA2, 90072183CA2, 90072191CA2 1289839 14 1289839CD1 35 1289839CB1 8698064CA2 5565648 15 5565648CD1 36 5565648CB1 2764456 16 2764456CD1 37 2764456CB1 5734806 17 5734806CD1 38 5734806CB1 7495168 18 7495168CD1 39 7495168CB1 7483131 19 7483131CD1 40 7483131CB1 4558650 20 4558650CD1 41 4558650CB1 7506195 21 7506195CD1 42 7506195CB1

[0518] TABLE 2 GenBank ID NO: Polypeptide SEQ Incyte or PROTEOME Probability ID NO: Polypeptide ID ID NO: Score Annotation 1 1351608CD1 g3170887 0.0 [Mus musculus] ubiquitin-protein ligase E3-alpha (Kwon, Y. T., et al. (1998) The mouse and human genes encoding the recognition component of the N-end rule pathway) Proc. Natl. Acad. Sci. U.S.A. 95: 7898-7903.) 2 4259314CD1 g11990422 8.2E−198 [Homo sapiens] MOP-4 3 3660046CD1 g12656270 0.0 [Mus musculus] ubiquitin-protein ligase Nedd4-2. Kamynina, E. et al. (2001) A novel mouse Nedd4 protein suppreses the activity of the epithelial Na+ channel. FASEB J. 15: 204-214. 4 3016416CD1 g4868435 3.1E−45 [Homo sapiens] apoptosis related protein APR-2 5 2133755CD1 g12248402 8.4E−281 [Homo sapiens] cisplatin resistance related protein CRR9p. Yamamoto, K. et al. (2001) Biochem. Biophys. Res. Commun. 280: 1148-1154. 6 5259957CD1 g1903384 3.7E−120 [Homo sapiens] preferentially expressed antigen of melanoma. Ikeda, H., et al. (1997) Characterization of an antigen that is recognized on a melanoma showing partial HLA loss by CTL expressing an NK inhibitory receptor. Immunity 6, 199-208. 7 55029783CD1 g8131896 1.7E−188 [Homo sapiens] bladder cancer overexpressed protein 8 8032202CD1 g9081879 4.3E−11 [Homo sapiens] nasopharyngeal carcinoma-related protein. He, Z. W., et al. (2000) Cloning of a novel gene associated with human nasopharyngeal carcinoma. Chin. Sci. Bull. 45, 2267-2272. 9 6937367CD1 g8650435 1.5E−299 [Mus musculus] RalGDS-like protein 3. Shao, H. and Andres, D. A. (2000) a novel RalGEF-like protein, RGL3, as a candidate effector for rit and Ras. J. Biol. Chem. 275, 26914-26924. 10 3876510CD1 g5870832 7.3E−259 [Mus musculus] skm-BOP1. Hwang, I. and Gottlieb, P. D. (1997) The Bop gene adjacent to the mouse CD8b gene encodes distinct zinc-finger proteins expressed in CTLs and in muscle. J. Immunol. 158, 1165-1174. 11 4900076CD1 g9392657 2.2E−158 [Homo sapiens] PR-domain containing protein 9. Jiang, G. L., and Huang, S. (2000) The yin-yang of PR-domain family genes in tumorigenesis. Histol. Histopathol. 15, 109-117. 12 1543848CD1 g4809026 3.2E−121 [Homo sapiens] suppressor of G2 allele of skp1 homolog; Sgt1. Kitagawa, K., et al. (1999) Mol. Cell 4, 21-33. 13 6254070CD1 g348918 2.5E−205 [Homo sapiens] hWNT5A. Clark, C. C. et al. (1993) Molecular cloning of the human proto-oncogene Wnt- 5A and mapping of the gene (WNT5A) to chromosome 3p14-p21. Genomics 18: 249-260. 14 1289839CD1 g1666073 1.7E−48 [Homo sapiens] RRP22 protein. Zucman-Rossi, J. et al. (1996) Identification of new members of the Gas2 and Ras families in the 22q12 chromosome region. Genomics 38: 247-254. 15 5565648CD1 g6164747 5.3E−36 [Homo sapiens] F-box protein Fbx22. (Cenciarelli, C. et al. (1999) Identification of a family of human F-box proteins. Curr. Biol. 9: 1177-1179.) 16 2764456CD1 g6630609 3.6E−252 [Homo sapiens] cyclin-E binding protein 1. (Mitsui, K. et al. (1999) A novel human gene encoding HECT domain and RCC1- ilke repeats interacts with cyclins and is potentially regulated by the tumor suppressor proteins. Biochem. Biophys. Res. Commun. 266: 115-122.) 17 5734806CD1 g5923891 0.0 [Homo sapiens] cyclophilin-related protein Anderson, S. K. et al. (1993) Proc. Natl. Acad. Sci. U.S.A. 90: 542-546. 18 7495168CD1 g13277570 6.0E−108 [Homo sapiens] (BC003694) tumor necrosis factor, alpha-induced protein 1 (endothelial) 19 7483131CD1 g2330015 8.3E−21 [Homo sapiens] apoptotic protease activating factor 1 (Apaf-1) Zou, H. et al. (1997) Cell 90, 405-413 20 4558650CD1 g4416181 2.4E−234 [Mus musculus] ES18 Park, E. J. et al. (1999) Nucleic Acids Res. 27, 1524-1530 21 7506195CD1 g4416181 5.2E−155 [Mus musculus] ES18 Park, E. J. et al. (1999) supra

[0519] TABLE 3 Analytical SEQ Incyte Amino Potential Potential Methods ID Polypeptide Acid Phosphorylation Glycosylation Signature Sequences, and NO: ID Residues Sites Sites Domains and Motifs Databases 1 1351608CD1 1738 S16 S100 S277 N281 N711 N750 Putative zinc finger HMMER_(—) S570 S586 S625 N785 N1043 in N-recognin PFAM S689 S715 S816 (a recognition component S833 S989 S993 of the N-end rule pathway): S1053 S1078 S1257 Q86-E156 S1272 S1278 S1489 S1582 S1605 T61 T162 T194 T250 T433 T480 T727 T752 T757 T787 T798 T882 T973 T1036 T1080 T1512 T1549 Y99 Y216 Y677 Transmembrane domains: TMAP V633-E651, F864-R881, S1278-L1295, I1378-Y1406, S1421-L1449, G1483-Y1507, G1640-R1660 UBIQUITIN PROTEIN LIGASE BLAST_(—) E3 COMPONEN PRODOM NRECOGNIN UBIQUITIN PROTEIN LIGASE E3ALPHA LIGASE PD149323: L1202-Y1485 LIGASE UBIQUITIN PROTEIN BLAST_(—) E3 COMPONENT PRODOM NENDRECOGNIZING N RECOGNIN UBIQUITIN CONJUGATION PD006492: A355-E897, T752-I1225, I341-L535, F24-S100 UBIQUITINPROTEIN LIGASE BLAST_(—) E3 COMPONEN PRODOM NRECOGNIN UBIQUITINPROTEIN LIGASE E3ALPHA LIGASE PD149312: M1-F85 LIGASE UBIQUITINPROTEIN BLAST_(—) E3 COMPONENT PRODOM NENDRECOGNIZING PROTEIN N RECOGNIN UBIQUITIN CONJUGATION PD010181: P37-Q284, P37-L329 Leucine zipper pattern: MOTIFS L593-L614 2 4259314CD1 389 S108 S149 S272 N143 N220 N257 ThiF family: A60-G200 HMMER_(—) S317 S340 S360 PFAM T25 T89 T93 T208 T209 T230 T246 T277 T293 T364 Y132 Transmembrane domain: TMAP G70-K86 N terminus is non-cytosolic. UBIQUITINACTIVATING ENZYME BLAST_(—) E1 UBIQUITIN CONJUGATION PRODOM LIGASE REPEAT MULTIGENE FAMILY PROTEIN PD005434: C197-E363 PROTEIN ENZYME BLAST_(—) UBIQUITINACTIVATING PRODOM UBIQUITIN E1 CONJUGATION LIGASE REPEAT BIOSYNTHESIS MULTIGENE PD000731: S62-F196 UBIQUITIN-ACTIVATING ENZYME BLAST_(—) DM00412|P22314|44-293: A35-Q290 DOMO DM00412|P20973|37-288: E38-I287 DM00412|P31252|40-291: S33-I287 DM00412|P22515|8-256: T34-I287 3 3660046CD1 854 S16 S104 S110 N59 N95 N287 HECT-domain (ubiquitin- HMMER_(—) S130 S182 S191 N569 transferase): F548-V853 PFAM S200 S214 S221 S268 S366 S510 S565 S638 S771 S832 T6 T154 T248 T402 T403 T437 T453 T505 T624 T648 T679 T784 Y688 WW domains: HMMER_(—) L266-P295, L378-P407, L74-P103, PFAM L429-P458 Transmembrane domain: TMAP F589-F610 WW/rsp5/WWP domain proteins: BLIMPS_(—) BL01159: Y89-P103 BLOCKS WW domain signature: BLIMPS_(—) PR00403: L378-R391, Y281-P295 PRINTS HECT-domain (ubiquitin- BLIMPS_(—) transferase): PFAM PF00632: F711-D717, W761-P788, L815-N846 PROTEIN LIGASE UBIQUITIN BLAST_(—) CONJUGATION REPEAT PRODOM UBIQUITINPROTEIN DNA BINDING PROBABLE ONCOGENIC PD002225: I623-F850, A543-L669 NEDD4 PROTEIN BLAST_(—) PD092083: S104-G265 PRODOM PD064436: I296-F377 PD033209: M1-S63 HECT DOMAIN BLAST_(—) DM01690|P39940|513-808: N556-F850 DOMO DM01690|P51593|9-306: N556-F850 DM01690|A38919|785-1082: F555-D851 DM01690|P53119|615-909: N556-D851 WW/rsp5/WWP domain signature: MOTIFS W78-P103, W270-P295, W382-P407, W433-P458 4 3016416CD1 111 S69 T88 signal_cleavage: M1-G26 SPSCAN 5 2133755CD1 538 S3 S84 S161 S219 N91 N101 N229 Signal Peptide: M1-T23 HMMER S231 S268 S317 S322 S387 S389 S491 S526 T60 T160 T385 T470 T476 Transmembrane domain: M1-Y28 TMAP T282-S310 T323- V349 Y429-K457 P465-R493 N-terminus is cytosolic. PROTEIN THYMIC EPITHELIAL BLAST_(—) CELL SURFACE ANTIGEN PRODOM R166.2 T13H5.2 PD025254: E87-P410 PROTEIN R166.2 T13H5.2 PD042934: BLAST_(—) L411-K530 PRODOM 6 5259957CD1 474 S2 S26 S45 S77 N155 N270 Leucine Rich Repeat: HMMER_(—) S80 S122 S128 Q320-L343, T349-S373, K99-P124 PFAM S192 S277 S305 S317 T27 T51 T139 T157 T439 MELANOMA PREFERENTIALLY BLAST_(—) EXPRESSED ANTIGEN KIAA0014 PRODOM PROTEIN DJ845O24.3 PRAME LIKE OF PD043129: L69-C472, A5-E125 7 55029783CD1 354 S12 S19 S168 S186 N84 N133 N138 Transmembrane domains: T73-L99 TMAP S341 T7 T15 N279 S116-S135 I176-V204 Y231-F251 W260-L280 T289-G309 S318- H337 N-terminus is cytosolic Cell attachment sequence: MOTIFS R39-D41 8 8032202CD1 272 S82 S226 T237 N36 N67 N95 N118 signal_cleavage: M1-A20 SPSCAN T256 Signal Peptide: M2-A20, M2-K23, HMMER M1-P25, M1-A32 Transmembrane domain: W6-R34 TMAP N-terminus is non-cytosolic 9 6937367CD1 710 S30 S36 S40 S170 N339 Ras association (RalGDS/AF-6) HMMER_(—) S221 S247 S277 domain: E613-G700 PFAM S342 S377 S388 S402 S495 S512 S520 S526 S540 S559 S580 S591 S601 T63 T99 T256 T290 T372 T522 T635 RasGEF domain: L244-K454 HMMER_(—) PFAM PROTEIN FACTOR RELEASING BLAST_(—) GUANINENUCLEOTIDE GUANINE PRODOM NUCLEOTIDE OF SH3 DOMAIN SON PD002030: L243-W456 LTE1 PROTEIN BLAST_(—) DM08605|A56234|4-495: L11-S499 DOMO GUANINE-NUCLEOTIDE BLAST_(—) DISSOCIATION STIMULATORS DOMO CDC25 FAMILY DM01741|P04821|1062-1534: L69-L393, V421-L498 10 3876510CD1 490 S128 S243 S251 N211 N257 MYND zinc finger: HMMER_(—) T183 T444 Y325 C52-C90 PFAM Y458 Transmembrane domain: I348-R376 TMAP N-terminus is cytosolic Zinc finger PF00642: BLIMPS_(—) L62-H72 PFAM PROTEIN ZINCFINGER BOP BLAST_(—) NUCLEAR DNABINDING PRODOM ALTERNATIVE SPLICING METALBINDING PD034977: E327-Q490 PD129736: E7-V51 PD129734: Q280-H326 PROTEIN ZINCFINGER BY BLAST_(—) 1EVEDENCE = PREDICTED PRODOM MATCH PUTATIVE BOPLIKE ORF YPL165C ZINC PD005436: A92-L287 11 4900076CD1 599 S80 S100 S181 N44 N311 KRAB box: HMMER_(—) S203 S277 S307 V62-S112 PFAM S333 S363 S389 S475 S503 S559 S587 T28 T33 T63 T72 T189 T235 T318 T346 T395 T430 Y325 Y437 Zinc finger, C2H2 type: HMMER_(—) Y437-H459, Y521-H543, Y325-H347, PFAM Y297-H319, Y577-H599, Y409-H431, Y549-H571, Y269-H291, Y465-H487, Y381-H403, Y493-H515, Y353-H375 Zinc finger, C2H2 type BL00028: BLIMPS_(—) C299-H315 PRINTS PROTEIN ZINC FINGER ZINC BLIMPS_(—) PD01066: F64-A102 PRODOM ZINC FINGER PROTEIN BLAST_(—) PD017719: P352-F586 PRODOM PD101192: A102-N242 PD000072: K295-C358 ZINC FINGER, C2H2 TYPE, BLAST_(—) DOMAIN DOMO DM00002|P08042|314-358: C358-H403, C526-H571, C442-H487 Zinc finger, C2H2 type, domain: MOTIFS C271-H291 C299-H319 C327-H347 C355-H375 C383-H403 C411-H431 C439-H459 C467-H487 C495-H515 C523-H543 C551-H571 C579-H599 12 1543848CD1 365 S11 S17 S161 S202 N77 N78 N146 signal_cleavage: M1-A68 SPSCAN S214 S239 S331 N159 N329 N343 T101 T126 T141 T234 T240 T265 Y47 TPR Domain: A45-N78, S79-T112 HMMER_(—) PFAM PROTEIN D1054.3 SGT1 PD022846: BLAST_(—) K194-Y365 PRODOM 13 6254070CD1 365 S7 S101 S198 S233 N99 N105 N297 signal_cleavage: M1-A22 SPSCAN T280 T337 T356 N311 Signal Peptide: M6-V25, M1-S30, HMMER M6-S30 wnt family: L53-K365 HMMER_(—) PFAM Transmembrane domain: S8-W32 TMAP N-terminus is non-cytosolic Wnt-1 family proteins. BL00246: BLIMPS_(—) G81-C100, G116-S150, W162-E186, BLOCKS M203-Y255, G319-C364 Wnt-1 family signature wnt1.prf: PROFILESCAN M203-K252 PROTEIN DEVELOPMENTAL BLAST_(—) GLYCOPROTEIN PRECURSOR PRODOM SIGNAL WNT1 WNT5A WNT2 EXTRACELLULAR MATRIX PD000810: D161-K365, L53-G267 WNT-1 FAMILY DM00403|Q06442|13-358: Q23- BLAST_(—) K365 DOMO WNT-1 FAMILY DM00403|P09544|26-348: L53- BLAST_(—) K365 DOMO WNT-1 FAMILY DM00403|P47793|24-351: Q41- BLAST_(—) K365 DOMO WNT-1 FAMILY DM00403|P34889|25-359: S30- BLAST_(—) K365 DOMO Wnt-1 family signature C223-C232 MOTIFS 14 1289839CD1 203 S159 T4 T37 T70 N142 Ras family: R6-M203 HMMER_(—) T105 T150 PFAM Transmembrane domain: C79-R107, TMAP N-terminus is non-cytosolic Transforming protein P21 RAS BLIMPS_(—) signature PR00449: S119-L132, PRINTS Y155-V177, Y5-Y26, V46-V68 RAS TRANSFORMING PROTEIN BLAST_(—) DM00006|S41960|3-148: R6-E157 DOMO RAS TRANSFORMING PROTEIN BLAST_(—) DM00006|I55401|3-148: R6-E157 DOMO RAS TRANSFORMING PROTEIN BLAST_(—) DM00006|P48555|8-153: Y5-E157 DOMO RAS TRANSFORMING PROTEIN BLAST_(—) DM00006|P11234|11-157: V2-E157 DOMO ATP/GTP-binding site motif A MOTIFS (P-loop) G11-S18 15 5565648CD1 403 S13 S113 S128 N198 N257 F-box domain: HMMER_(—) S162 S263 S401 S19-T67 PFAM T62 T127 T242 Transmembrane domain: TMAP A344-G361 N-terminus is cytosolic. 16 2764456CD1 1022 S46 S216 S224 N263 N865 HECT-domain (ubiquitin-transferase): HMMER_(—) S242 S290 S339 E726-V1015 PFAM S368 S385 S397 S647 S669 S690 S793 S801 S807 S867 S915 S975 S995 T17 T118 T124 T259 T319 T323 T362 T375 T398 T427 T431 T443 T448 T459 T550 T552 T729 T850 T904 T939 T951 T973 Y758 Regulator of chromosome HMMER_(—) condensation (RCC1): PFAM K93-K145, D254-H304, D146-L198, G200-Q253, R43-H92 Transmembrane domain: TMAP R757-K785 N-terminus is non-cytosolic. Regulator of chromosome BLIMPS_(—) condensation (RCC1) BLOCKS proteins: BL00625: G136-K164, V238-S271 Regulator of chromosome PROFILESCAN condensation (RCC1) signatures: rcc1_1.prf: V186-V238 rcc1_2.prf: A60-F112, G110-E165, P221-G269 Chromosome condensation regulator BLIMPS_(—) RCC1 signature: PRINTS PR00633: R95-E111, V149-E165, I241-V257 HECT-domain (ubiquitin-transferase) BLIMPS_(—) PF00632: V836-G842, L930-H957, PFAM H979-N1010 PROTEIN LIGASE UBIQUITIN BLAST_(—) CONJUGATION REPEAT PRODOM UBIQUITINPROTEIN DNA BINDING PROBABLE ONCOGENIC PD002225: V716-F1014 UBIQUITIN CONJUGATION BLAST_(—) PD136613: V348-L674, P68-G110, PRODOM P119-G163, E11-Q70, P227-G307, Q169-L228 PD071828: K164-L198 PROTEIN REPEAT GUANINE- BLAST_(—) NUCLEOTIDE RELEASING PRODOM FACTOR REGULATOR CELL CYCLE MITOSIS PD001424: K93-G163 HECT DOMAIN BLAST_(—) DM01690|P39940|513-808: F721-F1014 DOMO DM01690|P40985|578-891: P731-D905, V836-F1014, Q212-K226 DM01690|A38919|785-1082: Y758-F1014 DM01690|P53119|615-909: K755-F1014 Regulator of chromosome MOTIFS condensation (RCC1) signature 2: A28-L38, V80-V90, V133-L143, V186-L196, I241-L251 17 5734806CD1 1462 S145 S180 S206 N119 N203 N863 Cyclophilin-type peptidyl-prolyl HMMER_(—) S210 S212 S214 N870 N900 N937 cis-trans isomerase: S221 S235 S243 N1047 Q8-A177 PFAM S244 S260 S274 S328 S348 S350 S352 S383 S393 S394 S402 S462 S466 S470 S476 S483 S494 S495 S500 S502 S513 S517 S531 S553 S563 S565 S670 S681 S688 S695 S722 S747 S761 S766 S768 S773 S774 S776 S798 S802 S808 S820 S846 Transmembrane domain: P131-I150 TMAP S848 S855 S882 N-terminus is non-cytosolic S888 S890 S898 S906 S915 S917 S939 S949 S955 S957 S964 S1044 S1060 S1061 S1066 S1076 S1180 S1202 S1243 S1275 S1295 S1296 S1303 S1318 S1346 S1372 S1375 S1378 S1382 S1390 S1398 S1417 S1435 S1441 S1443 S1445 S1454 Cyclophilin-type peptidyl-prolyl BLIMPS_(—) S1458 T35 T53 cis-trans isomerase BLOCKS T126 T193 T337 signature BL00170: G21-K47, T419 T453 T471 Y59-N98, A106-I150 T859 T931 T989 T1049 T1057 T1082 T1207 T1252 T1283 Y90 Y1461 Cyclophilin-type peptidyl-prolyl PROFILESCAN cis-trans isomerase signature & profile: D30-D96 Cyclophilin peptidyl-prolyl BLIMPS_(—) cis-trans isomerase PRINTS signature PR00153: L27-L42, F64-G76, F107-Q122, Q122-D134, G135-I150 NK TUMOR RECOGNITION BLAST_(—) PROTEIN NATURAL KILLER PRODOM CELLS CYCLOPHILIN RELATED NKTR CYCLOSPORIN ISOMERASE ROTAMASE REPEAT TRANSMEMBRANE PD145736: N729-T1328 PD078637: G557-Y680 PD055818: C447-G530 ISOMERASE ROTAMASE BLAST_(—) CYCLOPHILIN CIS-TRANS PRODOM PEPTIDYL-PROLYL PPIASE CYCLOSPORIN MULTIGENE FAMILY PROTEIN PD000341: F11-L176 RECOGNITION; TUMOR; PROLYL; BLAST_(—) NATURAL; DM08077 DOMO |P30414|230-1403: L176-R1348 |B47328|230-1507: L176-Y1461 CYCLOPHILIN-TYPE PEPTIDYL- BLAST_(—) PROLYL CIS-TRANS ISOMERASE DOMO DM00129 |B47328|58-229: Q4-V175 |P30414|58-229: Q4-V175 Cyclophilin-type peptidyl-prolyl MOTIFS cis-trans isomerase signature: Y59-G76 18 7495168CD1 329 S22 S71 S89 S110 N176 K+ channel tetramerisation HMMER_(—) S155 S186 T55 T60 domain: K41-Q138 PFAM T143 T166 T187 T245 T250 T271 T315 PROTEIN EDP1 TUMOR BLAST_(—) NECROSIS FACTOR ALPHA- PRODOM INDUCED ENDOTHELIAL B12 PD037429: L118-D329 19 7483131CD1 476 S38 S128 S136 N150 N365 N460 signal_cleavage: M1-L30 SPSCAN S159 S175 S194 S333 S370 S439 S445 T7 T33 T164 T184 T268 T444 T462 SAM domain (Sterile alpha motif): HMMER_(—) E330-R394 WD domain, G-beta PFAM repeat: L4-S38, I273-Q309, Y231-D267, P46-N82, A90-N125, C172-I218, L131-D167 Trp-Asp (WD-40) repeats signature: PROFILESCAN L243-A290 Beta G-protein (transducin) BLIMPS_(—) signature PR00319: L235-G251, PRINTS L254-T268, I273-A288, P291-W308 G-protein beta WD-40 repeat signature PR00320: L69- T83, L296-F310 Trp-Asp (WD) repeats signature: MOTIFS L69-T83, L112-A126 20 4558650CD1 485 S119 S170 S343 signal_cleavage: M1-A68 SPSCAN S363 T153 T312 PROTEIN REPEAT SIGNAL BLAST_(—) PRECURSOR PRION PRODOM GLYCOPROTEIN NUCLEAR GPI ANCHOR BRAIN MAJOR PD001091: G10-P123 PROTEIN TYROSINE PHOSPHATASE TD14 EC 3.1.3.48 HYDROLASE PD180360: P4-R187, E323-K357 FORMIN; DM04565|Q05858|1-1212: P12-G115 BLAST_(—) FIBRILLAR COLLAGEN CARBOXYL- DOMO TERMINAL DM00042|A41132|43-133: P12-C95 DM00042|S21930|37-137: P12-F98 PROLINE-RICH PROTEIN DM03894|A39066|1- 159: P14-P129 21 7506195CD1 406 S119 S170 T153 signal_cleavage: M1-A68 SPSCAN T312 PROTEIN REPEAT SIGNAL BLAST_(—) PRECURSOR PRION PRODOM GLYCOPROTEIN NUCLEAR GPIANCHOR BRAIN MAJOR PD001091: G10-P123, R11-P129 FIBRILLAR COLLAGEN CARBOXYL- BLAST_(—) TERMINAL DM00042|A41132|43-133: P12-C95, DOMO P14-P117 FIBRILLAR COLLAGEN CARBOXYL- BLAST_(—) TERMINAL DM00042|S21930|37-137: P12-F98, DOMO P20-P120 PROLINE-RICH PROTEIN DM03894|A39066|1- BLAST_(—) 159: P14-P129 DOMO FORMIN; DM04565|Q05858|1-1212: P12-G115 BLAST_(—) DOMO

[0520] TABLE 4 Polynucleotide SEQ ID NO:/ Incyte ID/Sequence Length Sequence Fragments 22/1351608CB1/ 1-644, 1-733, 637-5226, 3489-3638, 3563-3836, 3661-4146, 4346-4436, 4349-4563, 4457-4914, 4545-4994, 4559-4972, 7742 4574-4755, 4635-4889, 4660-5217, 4678-4738, 4678-4816, 4683-4816, 4687-4824, 4689-4998, 4689-5130, 4689-5287, 4801-5354, 4802-4985, 4812-5178, 4818-5380, 4889-5124, 4896-5198, 4904-5425, 4929-5381, 4981-5151, 4981-5249, 4981-5565, 4993-5228, 5005-5380, 5098-5521, 5126-5401, 5127-5434, 5270-5519, 5271-5560, 5324-5605, 5384-5802, 5386-5992, 5431-5703, 5431-5881, 5431-5939, 5431-5944, 5431-6023, 5469-5733, 5499-5939, 5521-5677, 5596-6077, 5630-5831, 5739-6288, 5745-5984, 5748-5999, 5779-6051, 5799-6068, 5860-6312, 5910-6472, 5940-6491, 5954-6435, 5954-6459, 6135-6600, 6139-6600, 6188-6520, 6193-6462, 6227-6470, 6289-6832, 6290-6487, 6319-6582, 6333-6584, 6348-6625, 6401-6679, 6401-6916, 6441-6698, 6441-6802, 6443-6705, 6449-6702, 6470-6727, 6480-6727, 6502-6792, 6534-6869, 6588-6876, 6591-6864, 6591-6875, 6628-6835, 6671-6929, 6707-6880, 6711-7010, 6751-7095, 6778-7063, 6843-7113, 6855-7102, 6880-7134, 6899-7153, 6900-7186, 6947-7228, 6948-7200, 7030-7640, 7050-7638, 7087-7613, 7087-7622, 7091-7650, 7093-7634, 7105-7345, 7151-7631, 7161-7453, 7161-7649, 7161-7665, 7173-7650, 7176-7656, 7186-7659, 7192-7651, 7194-7650, 7199-7650, 7200-7653, 7202-7650, 7204-7650, 7214-7655, 7224-7650, 7228-7650, 7244-7498, 7249-7656, 7259-7650, 7268-7650, 7269-7655, 7269-7680, 7280-7650, 7292-7522, 7311-7650, 7316-7652, 7319-7650, 7322-7655, 7325-7650, 7331-7650, 7341-7650, 7353-7650, 7364-7659, 7380-7650, 7396-7653, 7399-7631, 7403-7647, 7412-7644, 7413-7663, 7414-7647, 7417-7607, 7417-7648, 7417-7661, 7417-7667, 7497-7650, 7502-7657, 7520-7652, 7533-7742, 7535-7656, 7592-7655 23/4259314CB1/ 1-73, 1-121, 1-138, 1-217, 1-337, 1-341, 1-363, 1-418, 1-430, 1-440, 1-463, 1-470, 1-476, 1-484, 1-494, 1-508, 1-513, 1674 1-521, 1-526, 1-628, 1-637, 2-252, 4-93, 4-246, 4-544, 4-588, 4-647, 4-681, 5-593, 5-604, 5-636, 16-526, 16-630, 20-476, 21-654, 77-680, 120-726, 195-778, 277-898, 411-1089, 442-1087, 534-1126, 535-1149, 551-1254, 562-819, 562-1060, 574-1166, 590-881, 591-1264, 670-1352, 673-1154, 677-1126, 696-1318, 721-1394, 726-980, 726-1151, 735-1336, 740-1456, 745-1126, 762-1456, 766-1252, 772-1213, 794-1456, 803-1289, 815-920, 887-1059, 893-1351, 897-1671, 900-1133, 927-1653, 961-1642, 968-1671, 1014-1633, 1033-1126, 1040-1641, 1054-1669, 1054-1674, 1055-1126, 1059-1126, 1059-1383, 1068-1650, 1161-1671, 1167-1671, 1179-1671, 1184-1674, 1191-1671, 1242-1656, 1259-1674 24/3660046CB1/ 1-827, 5-839, 11-599, 96-999, 237-558, 247-757, 348-932, 367-886, 376-2955, 438-700, 438-956, 633-1189, 648-1093, 3671 828-1461, 955-1153, 1404-1591, 1660-2067, 1682-3032, 1709-2307, 1841-2388, 1925-2601, 1937-2463, 1989-2760, 2076-2486, 2167-2759, 2263-3046, 2441-2705, 2574-3040, 2634-2899, 2734-3297, 2736-3248, 2764-3070, 2843-3052, 2853-3220, 2860-3338, 2911-3511, 3007-3655, 3013-3461, 3086-3367, 3094-3325, 3114-3671 25/3016416CB1/ 1-608, 170-2031, 371-608, 410-1096, 422-868, 429-963, 515-775, 515-1114, 519-1124, 579-926, 600-1266, 623-999, 2038 623-1222, 661-1207, 661-1284, 731-1290, 762-1339, 852-961, 866-961, 947-1534, 963-1165, 1016-1544, 1026-1582, 1034-1339, 1068-1232, 1095-1383, 1273-1550, 1273-1786, 1301-1864, 1327-1540, 1407-1686, 1425-1880, 1445-2021, 1484-1991, 1534-2003, 1581-1894, 1635-1904, 1639-1928, 1682-1992, 1682-1999, 1682-2038, 1697-1960, 1697-1971 26/2133755CB1/ 1-263, 69-584, 107-676, 107-718, 107-755, 109-300, 109-457, 109-480, 109-554, 109-566, 109-627, 109-657, 109-670, 2235 109-720, 109-786, 109-788, 109-885, 111-200, 111-276, 111-377, 111-518, 111-560, 111-575, 111-577, 111-606, 111-610, 111-652, 111-661, 111-680, 111-697, 111-706, 111-749, 111-770, 111-782, 111-788, 111-840, 112-207, 114-697, 116-841, 117-260, 118-401, 118-576, 119-635, 127-543, 127-592, 128-808, 131-736, 132-371, 132-378, 132-444, 132-541, 132-601, 132-609, 209-400, 222-478, 283-542, 350-574, 365-779, 375-601, 405-608, 405-624, 633-890, 661-905, 697-964, 717-970, 720-939, 720-958, 720-968, 723-1039, 744-1011, 763-1055, 771-1001, 808-1276, 840-1264, 845-1161, 848-1085, 865-1167, 875-1204, 904-1177, 904-1329, 914-1180, 918-1198, 923-1194, 923-1366, 927-1384, 930-1210, 943-1155, 948-1156, 950-1200, 950-1226, 951-1501, 952-1254, 959-1200, 968-1287, 971-1186, 971-1206, 974-1200, 984-1255, 984-1553, 994-1276, 997-1264, 1025-1294, 1030-1232, 1034-1261, 1036-1263, 1036-1316, 1042-1250, 1046-1319, 1047-1313, 1051-1282, 1056-1327, 1057-1276, 1060-1340, 1064-1317, 1077-1328, 1082-1335, 1085-1354, 1127-1372, 1128-1563, 1135-1398, 1145-1402, 1145-1413, 1156-1458, 1167-1461, 1168-1333, 1180-1389, 1189-1438, 1191-1478, 1194-1509, 1225-1455, 1225-1646, 1227-1487, 1245-1507, 1260-1508, 1261-1524, 1269-1515, 1271-1506, 1273-1411, 1273-1516, 1277-1537, 1302-1483, 1307-1883, 1337-1556, 1338-1538, 1338-1544, 1350-1608, 1350-1619, 1370-1635, 1377-1692, 1384-1641, 1390-1676, 1393-1646, 1394-1623, 1399-1646, 1400-1635, 1409-1678, 1418-1721, 1419-1698, 1430-1708, 1438-1674, 1439-1673, 1439-1960, 1443-1706, 1460-1725, 1460-1983, 1528-1718, 1557-2206, 1564-1815, 1565-1762, 1607-1811, 1611-1840, 1627-2201, 1633-1816, 1643-2214, 1654-1914, 1704-2220, 1803-2026, 1820-2048, 1820-2055, 1850-2120, 1850-2220, 1890-2108, 1893-2113, 1893-2133, 2003-2206, 2048-2219, 2053-2235 27/5259957CB1/ 1-346, 1-461, 1-478, 1-526, 1-569, 1-570, 53-550, 248-817, 259-709, 292-913, 312-820, 317-688, 346-919, 360-1014, 1851 361-926, 455-1063, 510-1126, 526-1093, 539-1080, 625-1201, 630-1263, 632-1215, 690-1182, 696-1164, 696-1319, 768-1303, 785-1219, 885-1468, 888-1245, 898-1354, 905-1083, 915-1171, 966-1442, 1074-1673, 1108-1701, 1210-1851, 1226-1531, 1232-1743, 1300-1830 28/55029783CB1/ 1-614, 110-817, 112-683, 117-675, 125-633, 126-647, 141-701, 141-765, 141-847, 141-851, 149-535, 149-700, 155-752, 1466 155-766, 155-783, 155-784, 164-827, 165-789, 168-835, 168-855, 168-862, 170-644, 173-194, 207-779, 215-748, 236-434, 272-743, 405-608, 429-1116, 454-710, 454-938, 467-1116, 471-718, 487-1277, 500-734, 503-1116, 519-1132, 560-745, 560-1369, 561-1305, 564-1132, 638-1369, 683-1342, 977-1211, 977-1466, 1066-1249, 1081-1298 29/8032202CB1/ 1-312, 1-655, 3-834, 256-974, 343-593, 343-594, 412-1049, 439-731, 439-909, 539-963 1049 30/6937367CB1/ 1-474, 3-121, 3-712, 44-314, 91-198, 91-206, 94-440, 175-600, 207-413, 210-675, 376-1202, 456-1090, 474-958, 2520 524-1054, 533-1119, 554-746, 596-1190, 613-1202, 646-1054, 726-1108, 750-871, 760-1281, 783-903, 808-1056, 849-1300, 878-1441, 919-1678, 985-1242, 1027-1388, 1128-1413, 1144-1688, 1158-1279, 1243-1512, 1243-1576, 1252-1449, 1268-1769, 1269-1581, 1331-1593, 1348-1418, 1351-1388, 1386-1421, 1408-1995, 1419-1463, 1419-1579, 1419-1631, 1419-1689, 1419-1707, 1419-1755, 1419-1789, 1419-1822, 1419-1866, 1419-1872, 1419-1971, 1419-2020, 1419-2058, 1436-1598, 1446-1637, 1452-1913, 1474-1664, 1474-1666, 1480-1943, 1482-1692, 1510-1959, 1543-1681, 1546-2072, 1585-2284, 1604-2123, 1604-2252, 1610-1762, 1617-1887, 1658-1926, 1716-2018, 1752-1951, 1752-2229, 1753-2027, 1770-2054, 1822-2234, 1835-2109, 1855-1996, 1855-2336, 1890-2187, 1933-2137, 1934-2497, 1979-2253, 2019-2520, 2073-2312, 2092-2296, 2120-2347 31/3876510CB1/ 1-619, 1-634, 6-322, 12-786, 14-140, 92-787, 147-463, 147-718, 147-865, 147-879, 147-917, 147-920, 147-927, 147-931, 4360 150-752, 150-860, 150-884, 164-473, 195-1051, 315-429, 315-532, 325-1145, 454-1042, 454-1045, 592-1493, 610-1485, 630-757, 700-1454, 701-913, 744-1032, 767-1457, 770-1457, 804-1126, 923-1154, 923-1375, 942-1197, 957-1239, 960-1241, 1114-1792, 1155-1179, 1164-1441, 1165-1804, 1171-1198, 1236-1703, 1249-1271, 1254-1588, 1321-1580, 1369-1865, 1456-1818, 1457-1751, 1466-1819, 1523-1734, 1727-1983, 1736-2047, 1813-2114, 1839-2115, 1858-2443, 1862-2154, 1863-2371, 1863-2384, 1863-2438, 1863-2498, 1886-2165, 1924-2426, 2023-2365, 2114-2394, 2114-2693, 2114-2805, 2114-2897, 2133-2663, 2176-2726, 2192-2473, 2200-2402, 2201-2438, 2235-2504, 2250-2832, 2352-2696, 2364-2598, 2364-2885, 2364-2910, 2364-2911, 2364-2976, 2364-2988, 2364-3032, 2364-3068, 2364-3069, 2364-3172, 2388-2660, 2389-2749, 2392-2749, 2397-3276, 2405-2696, 2444-3041, 2456-3159, 2463-2699, 2482-3112, 2490-3076, 2492-2732, 2516-3037, 2544-3174, 2557-3214, 2560-3109, 2562-2833, 2570-3277, 2588-3281, 2603-2816, 2606-2886, 2637-3118, 2640-3150, 2655-3152, 2676-3120, 2679-3362, 2694-3217, 2724-3161, 2728-3165, 2739-3205, 2744-3390, 2746-3418, 2756-3401, 2762-3217, 2762-3391, 2766-3182, 2768-3391, 2782-3398, 2801-3284, 2810-3007, 2810-3311, 2819-3289, 2856-3425, 2917-3425, 2942-3494, 2992-3445, 3005-3449, 3020-3672, 3029-3852, 3032-3652, 3040-3545, 3051-3594, 3063-3568, 3065-3555, 3080-3683, 3099-3612, 3113-3792, 3124-3613, 3152-3363, 3156-3626, 3194-3529, 3198-3466, 3213-3237, 3228-3792, 3252-3559, 3257-3971, 3266-3566, 3279-3535, 3296-3990, 3322-3849, 3335-3829, 3338-3956, 3349-3605, 3349-3793, 3349-3910, 3387-3889, 3404-4215, 3441-4333, 3455-4149, 3465-4055, 3479-4071, 3541-4037, 3553-4209, 3566-4133, 3589-3831, 3594-4209, 3646-4353, 3648-4223, 3649-4146, 3661-4161, 3687-3904, 3692-3944, 3693-4360, 3700-4104, 3706-3960, 3706-4157, 3706-4216, 3706-4250, 3706-4339, 3706-4355, 3723-3947, 3723-3950, 3734-3967, 3744-4323, 3749-4190, 3779-4273, 3794-4088, 3815-4346, 3835-4338, 3863-4346, 3868-4183, 3881-4357, 3891-4333, 3901-3936, 3907-4346, 3916-4345, 3918-4303, 3918-4358, 3921-4360, 3924-4346, 3933-4178, 3938-4358, 3953-4349, 3965-4347, 3986-4343, 3988-4360, 3998-4345, 4024-4343, 4035-4239, 4086-4354, 4133-4344, 4153-4342 32/4900076CB1/ 1-239, 1-242, 1-286, 101-246, 102-359, 105-273, 105-347, 105-407, 108-457, 196-312, 235-708, 319-519, 456-968, 3500 516-642, 643-954, 643-1023, 643-1119, 645-1281, 651-1281, 673-1281, 854-1325, 854-1338, 854-1341, 854-1386, 854-1508, 857-1323, 859-1555, 916-1534, 1035-1636, 1040-1618, 1059-1335, 1061-1276, 1065-1624, 1107-1519, 1114-1201, 1114-1237, 1114-1250, 1114-1392, 1114-1459, 1114-1463, 1114-1464, 1114-1477, 1114-1481, 1116-1759, 1123-1632, 1135-1235, 1135-1237, 1135-1241, 1135-1248, 1135-1272, 1135-1290, 1135-1300, 1135-1308, 1135-1328, 1135-1340, 1135-1342, 1135-1370, 1135-1380, 1135-1403, 1135-1405, 1135-1423, 1135-1435, 1135-1436, 1135-1456, 1135-1464, 1135-1508, 1135-1546, 1135-1548, 1135-1560, 1135-1627, 1135-1631, 1135-1632, 1135-1666, 1135-1715, 1147-1201, 1148-1405, 1149-1592, 1158-1256, 1158-1264, 1158-1289, 1158-1294, 1158-1329, 1158-1336, 1158-1542, 1158-1575, 1158-1582, 1158-1659, 1160-1332, 1182-1465, 1182-1632, 1187-1473, 1188-1477, 1188-1716, 1211-1464, 1211-1477, 1217-1287, 1217-1288, 1217-1316, 1217-1323, 1217-1424, 1217-1474, 1217-1540, 1217-1558, 1217-1575, 1217-1703, 1217-1728, 1217-1730, 1218-1405, 1218-1459, 1218-1477, 1218-1703, 1218-1772, 1219-1359, 1219-1405, 1219-1409, 1219-1416, 1219-1425, 1219-1465, 1219-1558, 1219-1592, 1219-1676, 1219-1722, 1233-1575, 1233-1591, 1235-1575, 1239-1733, 1240-1827, 1245-1477, 1249-1538, 1251-1575, 1263-1716, 1265-1883, 1266-1812, 1271-1416, 1271-1676, 1273-1518, 1281-1632, 1297-1772, 1298-1880, 1302-1541, 1302-1575, 1302-1735, 1302-1764, 1302-1812, 1303-1642, 1303-1687, 1303-1695, 1303-1772, 1303-1800, 1317-1632, 1319-1632, 1321-1575, 1323-1827, 1333-1918, 1347-1810, 1349-1967, 1356-1592, 1362-1592, 1362-1632, 1364-1884, 1368-1716, 1377-1896, 1383-1632, 1385-1832, 1386-1632, 1386-1876, 1387-1487, 1387-1522, 1387-1528, 1387-1575, 1387-1577, 1387-1584, 1387-1593, 1387-1594, 1387-1738, 1387-1759, 1387-1760, 1387-1870, 1387-1876, 1387-1884, 1387-2015, 1391-1968, 1401-1716, 1403-1716, 1404-1911, 1410-1632, 1417-1708, 1421-1718, 1422-1716, 1431-1884, 1441-2024, 1446-1676, 1446-1982, 1449-1810, 1461-1980, 1469-1716, 1469-1948, 1470-1716, 1470-1760, 1490-1716, 1490-1810, 1491-1984, 1492-2062, 32 1494-1600, 1494-1659, 1494-1661, 1494-1668, 1494-1676, 1494-1810, 1494-1832, 1494-1928, 1494-1968, 1494-2012, 1495-1832, 1501-1928, 1509-1982, 1515-1735, 1515-1760, 1515-1810, 1521-1668, 1523-2135, 1532-1760, 1532-2064, 1533-1884, 1534-1672, 1534-1695, 1534-1738, 1534-1750, 1534-1761, 1534-1762, 1534-1885, 1534-1927, 1534-1939, 1534-1947, 1534-2024, 1534-2052, 1538-2096, 1545-2064, 1549-2024, 1553-1764, 1553-1810, 1554-1810, 1554-2014, 1559-2239, 1569-1884, 1571-1884, 1573-1810, 1575-1982, 1575-2079, 1585-1874, 1590-1884, 1608-2062, 1608-2146, 1609-1885, 1616-1844, 1616-2131, 1617-1982, 1633-2155, 1637-1884, 1638-1884, 1638-2131, 1638-2146, 1639-1762, 1639-1827, 1639-1829, 1639-1836, 1639-1846, 1639-2002, 1639-2012, 1639-2122, 1639-2128, 1639-2136, 1643-2146, 1651-2011, 1652-2162, 1653-1982, 1655-1982, 1657-1884, 1659-2062, 1659-2136, 1677-2294, 1683-1947, 1683-1969, 1683-1982, 1690-2294, 1691-2136, 1708-1928, 1708-2146, 1713-2150, 1722-1940, 1722-1982, 1722-2012, 1722-2098, 1742-2294, 1743-2146, 1744-2150, 1746-1982, 1782-2291, 1785-2012, 1785-2062, 1785-2136, 1785-2146, 1786-1924, 1786-1942, 1786-1947, 1786-1993, 1786-1997, 1786-2002, 1786-2013, 1786-2014, 1786-2136, 1786-2149, 1786-2154, 1788-2012, 1788-2123, 1797-2136, 1801-2123, 1805-1863, 1805-1869, 1805-1911, 1805-1912, 1805-1920, 1805-1928, 1805-2014, 1805-2062, 1805-2095, 1805-2107, 1805-2150, 1805-2162, 1806-2062, 1806-2150, 1818-2294, 1823-2294, 1824-2136, 1825-2062, 1827-2136, 1837-2126, 1839-2294, 1851-2150, 1853-2162, 1860-2002, 1861-2136, 1866-2096, 1866-2136, 1869-1948, 1869-2146, 1888-2136, 1889-2294, 1890-2136, 1890-2137, 1890-2146, 1890-2162, 1890-2353, 1890-2433, 1891-1948, 1891-2020, 1891-2024, 1891-2079, 1891-2081, 1891-2088, 1891-2097, 1891-2131, 1891-2135, 1891-2136, 1891-2160, 1905-2146, 1907-2146, 1909-2294, 1913-2150, 1914-2136, 1914-2146, 1920-2150, 1929-2136, 1935-2136, 1935-2146, 1952-2162, 1956-2136, 1957-2149, 1957-2150, 1961-2149, 1965-2136, 1974-2088, 1974-2146, 1974-2160, 1974-2162, 1989-2150, 1991-2150, 1994-2136, 1995-2162, 1996-2136, 1998-2146, 2034-2136, 2037-2146, 2037-2150, 2037-2162, 2038-2125, 2040-2149, 2049-2136, 2053-2136, 2057-2150, 2058-2136, 2058-2150, 2076-2136, 2077-2150, 2079-2146, 2079-2149, 2094-2136, 2113-2149, 2256-2450, 2269-2529, 2269-2859, 2293-2585, 2372-2423, 2372-2429, 2389-2706, 2391-2689, 2409-2668, 2463-2708, 2465-2715, 2518-2814, 2567-3163, 2727-3405, 2752-3404, 2766-3401, 2815-3067, 2818-3452, 2901-3133, 2901-3167, 2962-3457, 3003-3248, 3103-3487, 3276-3500 33/1543848CB1/1366 1-352, 135-672, 146-819, 160-873, 174-428, 174-439, 174-440, 174-456, 185-304, 185-352, 185-359, 185-361, 185-366, 185-401, 185-423, 185-431, 185-442, 185-445, 185-451, 185-468, 185-521, 185-560, 186-298, 187-432, 190-435, 192-435, 194-414, 194-476, 199-303, 199-459, 200-430, 200-443, 200-453, 200-457, 200-465, 200-472, 201-373, 201-426, 203-359, 206-583, 207-499, 209-393, 212-491, 213-460, 213-465, 215-294, 215-352, 215-353, 221-442, 222-392, 222-518, 225-724, 227-583, 228-348, 230-490, 241-805, 243-491, 250-352, 251-442, 253-501, 253-513, 258-357, 258-522, 258-528, 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3838-4113, 3850-4106, 3857-4113, 3874-4102, 3895-4103, 3977-4111 38/5734806CB1/ 1-789, 1-7058, 454-485, 488-716, 488-959, 488-1017, 491-1035, 524-753, 713-1374, 1025-1321, 1236-1847, 1268-1516, 7058 1284-1543, 1290-1695, 1302-1585, 1310-1860, 1318-2019, 1329-1557, 1350-1952, 1383-1561, 1390-1643, 1392-1943, 1403-1664, 1432-1804, 1483-1776, 1484-1789, 1484-1800, 1488-2101, 1489-1775, 1521-1777, 1562-1815, 1584-1881, 1597-1882, 1614-2220, 1636-2100, 1676-2074, 1697-1989, 1740-2046, 1741-2004, 1759-2059, 1768-2045, 1774-2079, 1832-2102, 1840-2386, 1845-2120, 1847-2088, 1853-2099, 1857-2138, 1888-2370, 2009-2277, 2040-2313, 2090-2586, 2092-2352, 2104-2386, 2108-2327, 2181-2434, 2200-2804, 2265-2962, 2270-2915, 2282-2926, 2294-2516, 2329-2595, 2332-2612, 2355-2582, 2359-2614, 2360-3027, 2445-2722, 2484-3041, 2525-3158, 2543-3133, 2636-2940, 2642-3238, 2647-3103, 2651-2932, 2678-2885, 2729-3077, 2737-3015, 2737-3117, 2739-3039, 2739-3103, 2740-3310, 2754-3368, 2807-3148, 2850-3308, 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39/7495168CB1/ 1-423, 1-481, 359-697, 367-714, 367-1024, 369-707, 369-713, 369-714, 369-1000, 376-1038, 382-779, 384-755, 389-765, 1380 395-624, 406-714, 407-697, 431-605, 431-664, 453-876, 458-951, 469-1082, 488-900, 491-1129, 495-949, 512-1107, 512-1182, 532-1183, 536-807, 540-1125, 559-1075, 559-1183, 561-1152, 575-804, 575-1152, 582-961, 590-1162, 636-1067, 640-907, 659-926, 661-1221, 668-1252, 701-927, 702-1027, 705-1239, 724-955, 728-1017, 796-1049, 888-1327, 891-1114, 927-1121, 931-1380 40/7483131CB1/ 1-600, 4-320, 19-510, 45-464, 53-291, 60-642, 63-336, 63-586, 163-447, 189-447, 255-567, 294-812, 294-830, 403-623, 1773 460-737, 473-951, 475-617, 516-642, 572-750, 606-854, 616-886, 628-876, 693-987, 695-972, 757-1354, 869-1101, 870-1400, 886-1131, 925-1675, 931-1166, 931-1441, 963-1559, 992-1308, 997-1269, 1020-1296, 1038-1357, 1098-1669, 1105-1711, 1172-1422, 1176-1701, 1185-1685, 1191-1332, 1192-1709, 1192-1713, 1195-1332, 1252-1723, 1255-1723, 1258-1721, 1274-1721, 1289-1728, 1290-1500, 1290-1645, 1295-1721, 1300-1705, 1302-1773, 1306-1585, 1306-1724, 1307-1584, 1311-1447, 1311-1734, 1316-1722, 1332-1724, 1336-1724, 1338-1721, 1339-1574, 1347-1610, 1347-1721, 1347-1724, 1349-1590, 1393-1717 41/4558650CB1/ 1-444, 78-452, 79-509, 100-453, 140-799, 163-462, 359-823, 455-699, 455-722, 455-818, 455-869, 455-887, 455-931, 2810 455-938, 455-944, 456-874, 460-1062, 464-879, 464-925, 464-985, 464-989, 464-1003, 464-1058, 466-905, 466-1129, 469-933, 473-942, 482-940, 489-880, 491-647, 491-673, 491-798, 499-877, 528-710, 642-1253, 643-1159, 842-1158, 900-1320, 907-1181, 929-1297, 930-1180, 930-1316, 955-1315, 958-1313, 983-1325, 993-1301, 998-1256, 999-1611, 1030-1290, 1064-1309, 1078-1280, 1078-1325, 1086-1283, 1107-1369, 1125-1309, 1125-1325, 1141-1325, 1332-1931, 1333-1731, 1334-1589, 1355-1624, 1361-1593, 1376-1721, 1385-1730, 1394-1797, 1394-1943, 1411-1876, 1438-1705, 1438-2022, 1439-1685, 1471-2032, 1498-1616, 1560-1834, 1600-1985, 1612-2088, 1622-2278, 1675-1928, 1779-2342, 1851-2345, 1855-2128, 1856-2119, 1915-2565, 1926-2532, 1933-2230, 1933-2261, 1942-2531, 1945-2453, 1945-2482, 1961-2531, 1965-2174, 1989-2766, 1996-2602, 1997-2488, 1999-2488, 2011-2459, 2041-2242, 2071-2300, 2086-2351, 2113-2373, 2114-2348, 2116-2368, 2116-2633, 2117-2715, 2133-2325, 2140-2363, 2146-2665, 2147-2766, 2151-2410, 2184-2731, 2259-2778, 2286-2602, 2324-2810, 2331-2465, 2344-2596, 2346-2810, 2356-2810, 2401-2474 42/7506195CB1/ 1-234, 11-454, 11-2549, 88-184, 88-310, 88-459, 88-462, 88-466, 89-519, 110-199, 110-463, 150-809, 164-462, 173-472, 2549 279-462, 369-833, 465-709, 465-732, 465-828, 465-879, 465-897, 465-941, 465-948, 465-954, 466-884, 470-1072, 474-889, 474-935, 474-995, 474-999, 474-1013, 474-1068, 476-915, 476-1139, 479-943, 483-952, 492-950, 499-890, 501-657, 501-683, 501-808, 509-887, 538-720, 653-1159, 760-1358, 852-1157, 949-1325, 1155-1503, 1158-1366, 1158-1397, 1158-1494, 1167-1570, 1167-1716, 1184-1649, 1211-1478, 1211-1795, 1212-1458, 1244-1805, 1271-1389, 1314-1905, 1315-1722, 1315-1877, 1316-1927, 1333-1607, 1373-1758, 1381-1726, 1381-1737, 1385-1861, 1448-1701, 1508-2074, 1552-2115, 1605-1777, 1624-2118, 1628-1901, 1629-1892, 1699-2305, 1706-2003, 1706-2034, 1715-2304, 1718-2226, 1718-2255, 1734-2304, 1738-1947, 1742-2099, 1751-2253, 1762-2539, 1769-2221, 1769-2375, 1770-2261, 1772-2261, 1784-2232, 1814-2015, 1844-2073, 1859-2124, 1886-2146, 1887-2121, 1889-2141, 1889-2406, 1890-2488, 1906-2098, 1913-2136, 1920-2539, 1924-2183, 1944-2236, 1957-2504, 2032-2549, 2059-2375, 2069-2238, 2097-2549, 2104-2238, 2117-2369, 2174-2247

[0521] TABLE 5 Polynucleotide SEQ ID NO: Incyte Project ID: Representative Library 22 1351608CB1 PGANNOT01 23 4259314CB1 STOMTMR02 24 3660046CB1 BRAIUNF01 25 3016416CB1 THYRDIE01 26 2133755CB1 SINTFER02 27 5259957CB1 KIDETXS02 28 55029783CB1 BLADTUT04 29 8032202CB1 TESTNOT11 30 6937367CB1 FTUBTUR01 31 3876510CB1 HEARFET02 32 4900076CB1 HNT2TXT01 33 1543848CB1 MPHGNOT03 34 6254070CB1 LUNPTUT02 35 1289839CB1 BRAHTDR04 36 5565648CB1 LIVRFET05 37 2764456CB1 COLNNOT23 38 5734806CB1 THYMNOR02 39 7495168CB1 NOSETUE01 40 7483131CB1 KIDNNOT19 41 4558650CB1 BRAUNOR01 42 7506195CB1 CONNTUT05

[0522] TABLE 6 Library Vector Library Description BLADTUT04 pINCY Library was constructed using RNA isolated from bladder tumor tissue removed from a 60-year-old Caucasian male during a radical cystectomy, prostatectomy, and vasectomy. Pathology indicated grade 3 transitional cell carcinoma in the left bladder wall. Carcinoma in-situ was identified in the dome and trigone. Patient history included tobacco use. Family history included type I diabetes, malignant neoplasm of the stomach, atherosclerotic coronary artery disease, and acute myocardial infarction. BRAHTDR04 PCDNA2.1 This random primed library was constructed using RNA isolated archaecortex, anterior hippocampus tissue removed from a 55-year-old Caucasian female who died from cholangiocarcinoma. Pathology indicatedmild meningeal fibrosis predominately over the convexities, scattered axonal spheroids in the white matter of the cingulate cortex and the thalamus, and a few scattered neurofibrillary tangles in the entorhinal cortex and the periaqueductal gray region. Pathology for the associated tumor tissue indicated well-differentiated cholangiocarcinoma of the liver with residual or relapsed tumor. Patient history included cholangiocarcinoma, post-operative Budd-Chiari syndrome, biliary ascites, hydrothorax, dehydration, malnutrition, oliguria and acute renal failure. Previous surgeries included cholecystectomy and resection of 85% of the liver. BRAIUNF01 PRARE This 5′ cap isolated full-length library was constructed using RNA isolated from a DU 145 cell line derived from a brain tumor removed from a 69-year-old Caucasian male. The cells were untreated for 14 hours. Pathology indicated metastatic carcinoma. Patient history included lymphocytic leukemia for 3 years and prostate carcinoma with metastasis to the brain. BRAUNOR01 pINCY This random primed library was constructed using RNA isolated from striatum, globus pallidus and posterior putamen tissue removed from an 81-year-old Caucasian female who died from a hemorrhage and ruptured thoracic aorta due to atherosclerosis. Pathology indicated moderate atherosclerosis involving the internal carotids, bilaterally; microscopic infarcts of the frontal cortex and hippocampus; and scattered diffuse amyloid plaques and neurofibrillary tangles, consistent with age. Grossly, the leptomeninges showed only mild thickening and hyalinization along the superior sagittal sinus. The remainder of the leptomeninges was thin and contained some congested blood vessels. Mild atrophy was found mostly in the frontal poles and lobes, and temporal lobes, bilaterally. Microscopically, there were pairs of Alzheimer type II astrocytes within the deep layers of the neocortex. There was increased satellitosis around neurons in the deep gray matter in the middle frontal cortex. The amygdala contained rare diffuse plaques and neurofibrillary tangles. The posterior hippocampus contained a microscopic area of cystic cavitation with hemosiderin-laden macrophages surrounded by reactive gliosis. Patient history included sepsis, cholangitis, post-operative atelectasis, pneumonia CAD, cardiomegaly due to left ventricular hypertrophy, splenomegaly, arteriolonephrosclerosis, nodular colloidal goiter, emphysema, CHF, hypothyroidism, and peripheral vascular disease. COLNNOT23 pINCY Library was constructed using RNA isolated from diseased colon tissue removed from a 16-year-old Caucasian male during a total colectomy with abdominal/perineal resection. Pathology indicated gastritis and pancolonitis consistent with the acute phase of ulcerative colitis. Inflammation was more severe in the transverse colon, with inflammation confined to the mucosa. There was only mild involvement of the ascending and sigmoid colon, and no significant involvement of the cecum, rectum, or terminal ileum. Family history included irritable bowel syndrome. CONNTUT05 pINCY Library was constructed using RNA isolated from tumorous skull soft tissue removed from a 34-year-old Caucasian female during skull lesion excision. Pathology indicated grade 3 ependymoma forming an implant in the dermis and subcutis associated with dense fibrosis. Patient history included seizures, bone cancer, and brain cancer. Surgeries included cranioplasty and cerebral meninges lesion excision, and treatment included whole brain radiation. Family history included anxiety and depression. FTUBTUR01 PCDNA2.1 This random primed library was constructed using RNA isolated from fallopian tube tumor tissue removed from an 85-year-old Caucasian female during bilateral salpingo-oophorectomy and hysterectomy. Pathology indicated poorly differentiated mixed endometrioid (80%) and serous (20%) adenocarcinoma, which was confined to the mucosa without mural involvement. Endometrioid carcinoma in situ was also present. Pathology for the associated uterus tumor indicated focal endometrioid adenocarcinoma in situ and moderately differentiated invasive adenocarcinoma arising in an endometrial polyp. Metastatic endometrioid and serous adenocarcinoma was present at the cul-de-sac tumor. Patient history included medullary carcinoma of the thyroid and myocardial infarction. HEARFET02 pINCY Library was constructed using RNA isolated from heart tissue removed from a Caucasian male fetus, who was stillborn with a hypoplastic left heart and died at 23 weeks' gestation. HNT2TXT01 pINCY Library was constructed using RNA isolated from the hNT2 cell line (derived from a human teratocarcinoma that exhibited properties characteristic of a committed neuronal precursor). Cells were treated with mouse leptin at 1 ug/ml and 9 cis retinoic acid at 3.3 uM for 6 days. KIDETXS02 pINCY This subtracted, transformed embryonal cell line library was constructed using 9 million clones from a treated, transformed embryonal cell line (293-EBNA) derived from kidney epithelial tissue and was subjected to two rounds of subtraction hybridization with 1.9 million clones from an untreated transformed embryonal cell line (293-EBNA) derived from a kidney epithelial tissue library. The starting library for subtraction was constructed using RNA isolated from the treated, transformed embryonal cell line (293-EBNA). The cells were treated with 5-aza-2′-deoxycytidine and transformed with adenovirus 5 DNA. The hybridization probe for subtraction was derived from a similarly constructed library from RNA isolated from untreated 293-EBNA cells from the same cell line. Subtractive hybridization conditions were based on the methodologies of Swaroop et al., NAR 19 (1991): 1954 and Bonaldo, et al. Genome Research (1996) 6: 791. KIDNNOT19 pINCY Library was constructed using RNA isolated from kidney tissue removed a 65-year-old Caucasian male during an exploratory laparotomy and nephroureterectomy. Pathology for the associated tumor tissue indicated a grade 1 renal cell carcinoma within the upper pole of the left kidney. Patient history included malignant melanoma of the abdominal skin, benign neoplasm of colon, cerebrovascular disease, and umbilical hernia. Family history included myocardial infarction, atherosclerotic coronary artery disease, cerebrovascular disease, prostate cancer, myocardial infarction, and atherosclerotic coronary artery disease. LIVRFET05 pINCY Library was constructed using RNA isolated from CD34+ progenitor cell tissue removed from the liver of a Caucasian male fetus who died after 20 weeks' gestation. LUNPTUT02 pINCY Library was constructed using RNA isolated from pleura tumor tissue removed from a 55-year-old Caucasian female during complete pneumonectomy. Pathology indicated grade 3 sarcoma most consistent with leiomyosarcoma, uterine primary, forming a bosellated mass replacing the right lower lobe and a portion of the middle lobe. The tumor involved the adjacent parietal pleura and pericardium. Multiple nodules comprising the tumor show near total necrosis. The right upper lobe was atelectic but uninvolved by tumor. Microsections of cellular nodules show brisk mitotic activity. The pericardium shows direct involvement but its margins were tumor free. Smooth muscle actin was positive. Estrogen receptor was negative and progesterone receptor was positive. Patient history included shortness of breath, peptic ulcer disease, lung cancer, uterine cancer, normal delivery, tobacco abuse, and deficiency anemia. Previous surgeries included endoscopic excision of a lung lesion. Family history included atherosclerotic coronary artery disease, breast cancer, type II diabetes, and multiple sclerosis. MPHGNOT03 PBLUESCRIPT Library was constructed using RNA isolated from plastic adherent mononuclear cells isolated from buffy coat units obtained from unrelated male and female donors. NOSETUE01 PCDNA2.1 This 5′ biased random primed library was constructed using RNA isolated from nasal and cribriform tumor tissue removed from a 45-year-old Caucasian male during total face ostectomy with reconstruction, rhinotomy and craniotomy. Pathology indicated olfactory neuroblastoma in the nasal cavity and cribriform region. The patient presented with cancer of the head, face and neck, and epistaxis. Patient history included extrinsic asthma, cancer of the head, face and neck, and epistaxis. Previous surgeries included total face ostectomy with reconstruction. Patient medications included Biaxin, Atessalon, and Valium. The patient received radiation treatments. Family history included chronic sinusitis in the mother and type II diabetes in the father. PGANNOT01 PSPORT1 Library was constructed using RNA isolated from paraganglionic tumor tissue removed from the intra-abdominal region of a 46-year-old Caucasian male during exploratory laparotomy. Pathology indicated a benign paraganglioma and was associated with a grade 2 renal cell carcinoma, clear cell type, which did not penetrate the capsule. Surgical margins were negative for tumor. SINTFER02 pINCY This random primed library was constructed using RNA isolated from small intestine tissue removed from a Caucasian male fetus who died from fetal demise. STOMTMR02 PCDNA2.1 This random primed library was constructed using RNA isolated from diseased stomach tissue removed from a 76-year-old Caucasian male during proximal gastrectomy and partial esophagectomy. Pathology indicated chronic gastritis. Pathology for the matched tumor tissue indicated invasive grade 3 adenocarcinoma forming an ulcerated mass at the gastro-esophageal junction. The tumor infiltrated through the muscularis propria into the periesophageal adipose tissue. One of four perigastric lymph nodes was positive for tumor. Patient history included dysphagia, atherosclerotic coronary artery disease, malignant melanoma of the skin, COPD, benign neoplasm of the large bowel, malignant neoplasm of upper lobe of lung, and alcohol abuse. Family history included atherosclerotic coronary artery disease and myocardial infarction. TESTNOT11 pINCY Library was constructed using RNA isolated from testicular tissue removed from a 16-year-old Caucasian male who died from hanging. Patient history included drug use (tobacco, marijuana, and cocaine use), and medications included Lithium, Ritalin, and Paxil. THYMNOR02 pINCY The library was constructed using RNA isolated from thymus tissue removed from a 2-year-old Caucasian female during a thymectomy and patch closure of left atrioventricular fistula. Pathology indicated there was no gross abnormality of the thymus. The patient presented with congenital heart abnormalities. Patient history included double inlet left ventricle and a rudimentary right ventricle, pulmonary hypertension, cyanosis, subaortic stenosis, seizures, and a fracture of the skull base. Family history included reflux neuropathy. THYRDIE01 PCDNA2.1 This 5′ biased random primed library was constructed using RNA isolated from diseased thyroid tissue removed from a 22-year-old Caucasian female during closed thyroid biopsy, partial thyroidectomy, and regional lymph node excision. Pathology indicated adenomatous hyperplasia. The patient presented with malignant neoplasm of the thyroid. Patient history included normal delivery, alcohol abuse, and tobacco abuse. Previous surgeries included myringotomy. Patient medications included an unspecified type of birth control pills. Family history included hyperlipidemia and depressive disorder in the mother; and benign hypertension, congestive heart failure, and chronic leukemia in the grandparent(s).

[0523] TABLE 7 Program Description Reference Parameter Threshold ABI A program that removes vector sequences and Applied Biosystems, Foster City, CA. FACTURA masks ambiguous bases in nucleic acid sequences. ABI/ A Fast Data Finder useful in comparing and Applied Biosystems, Foster City, CA; Mismatch <50% PARACEL annotating amino acid or nucleic acid sequences. Paracel Inc., Pasadena, CA. FDF ABI A program that assembles nucleic acid sequences. Applied Biosystems, Foster City, CA. AutoAssembler BLAST A Basic Local Alignment Search Tool useful in Altschul, S. F. et al. (1990) J. Mol. Biol. ESTs: Probability value = 1.0E−8 sequence similarity search for amino acid and 215: 403-410; Altschul, S. F. et al. (1997) or less; Full Length sequences: nucleic acid sequences. BLAST includes five Nucleic Acids Res. 25: 3389-3402. Probability value = 1.0E−10 or functions: blastp, blastn, blastx, less tblastn, and tblastx. FASTA A Pearson and Lipman algorithm that searches for Pearson, W. R. and D. J. Lipman (1988) ESTs: fasta E value = 1.06E−6; similarity between a query sequence and a group Proc. Natl. Acad Sci. USA 85: 2444-2448; Assembled ESTs: fasta Identity = of sequences of the same type. FASTA comprises Pearson, W. R. (1990) Methods Enzymol. 95% or greater and Match as least five functions: fasta, tfasta, fastx, tfastx, 183: 63-98; and Smith, T. F. and length = 200 bases or greater; and ssearch. M. S. Waterman (1981) Adv. Appl. Math. fastx E value = 1.0E−8 or less; 2: 482-489. Full Length sequences: fastx score = 100 or greater BLIMPS A BLocks IMProved Searcher that matches a Henikoff, S. and J. G. Henikoff (1991) Probability value = 1.0E−3 or less sequence against those in BLOCKS, PRINTS, Nucleic Acids Res. 19: 6565-6572; DOMO, PRODOM, and PFAM databases Henikoff, J. G. and S. Henikoff (1996) to search for gene families, sequence homology, Methods Enzymol. 266: 88-105; and and structural fingerprint regions. Attwood, T. K. et al. (1997) J. Chem. Inf. Comput. Sci. HMMER An algorithm for searching a query sequence 37: 417-424. Krogh, A. et al. (1994) J. Mol. PFAM, SMART or TIGRFAM Biol. against hidden Markov model (HMM)-based 235: 1501-1531; Sonnhammer, E. L. L. et hits: Probability value = 1.0E−3 databases of protein family consensus al. (1988) Nucleic Acids Res. 26: 320-322; or less; Signal peptide hits: sequences, such as PFAM, SMART Durbin, R. et al. (1998) Our World View, in Score = 0 or greater and TIGRFAM. a Nutshell, Cambridge Univ. Press, pp. 1-350. ProfileScan An algorithm that searches for structural and Gribskov, M. et al. (1988) CABIOS 4: Normalized quality score ≧ GCG- sequence motifs in protein sequences that match 61-66; Gribskov, M. et al. (1989) Methods specified “HIGH” value for that sequence patterns defined in Prosite. Enzymol. 183: 146-159; Bairoch, A. et al. particular Prosite motif. (1997) Nucleic Acids Res. 25: 217-221. Generally, score = 1.4-2.1. Phred A base-calling algorithm that examines automated Ewing, B. et al. (1998) Genome Res. sequencer traces with high sensitivity and 8: 175-185; Ewing, B. and probability. P. Green (1998) Genome Res. 8: 186-194. Phrap A Phils Revised Assembly Program including Smith, T. F. and M. S. Waterman (1981) Score = 120 or greater; Match SWAT and CrossMatch, programs based on Adv. Appl. Math. 2: 482-489; Smith, T. F. length = 56 or greater efficient implementation of the Smith- and M. S. Waterman (1981) J. Mol. Biol. 147: Waterman algorithm, useful in 195-197; and Green, searching sequence homology P., University of Washington, Seattle, WA. and assembling DNA sequences. Consed A graphical tool for viewing and editing Phrap Gordon, D. et al. (1998) Genome Res. assemblies. 8: 195-202. SPScan A weight matrix analysis program that scans Nielson, H. et al. (1997) Protein Engineering Score = 3.5 or greater protein sequences for the presence 10: 1-6; Claverie, J. M. and S. Audic (1997) of secretory signal peptides. CABIOS 12: 431-439. TMAP A program that uses weight matrices to delineate Persson, B. and P. Argos (1994) J. Mol. transmembrane segments on protein sequences Biol. 237: 182-192; Persson, B. and and determine orientation. P. Argos (1996) Protein Sci. 5: 363-371. TMHMMER A program that uses a hidden Markov Sonnhammer, E. L. et al. (1998) Proc. Sixth model (HMM) to delineate transmembrane Intl. Conf. On Intelligent Systems for Mol. segments on protein sequences Biol., Glasgow et al., eds., The Am. Assoc. and determine orientation. for Artificial Intelligence (AAAI) Press, Menlo Park, CA, and MIT Press, Cambridge, MA, pp. 175-182. Motifs A program that searches amino acid sequences for Bairoch, A. et al. (1997) Nucleic Acids Res. patterns that matched those defined in Prosite. 25: 217-221; Wisconsin Package Program Manual, version 9, page M51-59, Genetics Computer Group, Madison, WI.

[0524] TABLE 8 SEQ Caucasian African Asian Hispanic ID EST CB1 EST Allele Allele Amino Allele 1 Allele 1 Allele 1 Allele 1 NO: PID EST ID SNP ID SNP SNP Allele 1 2 Acid frequency frequency frequency frequency 42 7506195 6753167J1 SNP00121036 111 584 A A G Q145 n/d n/a n/a n/a 42 7506195 6763024J1 SNP00121036 111 584 A A G Q145 n/d n/a n/a n/a 42 7506195 6767449J1 SNP00121036 110 584 G A G R145 n/d n/a n/a n/a 42 7506195 6769029J1 SNP00121036 109 584 G A G R145 n/d n/a n/a n/a 42 7506195 7754321H1 SNP00121036 215 420 A A G P90 n/d n/a n/a n/a

[0525]

1 42 1 1738 PRT Homo sapiens misc_feature Incyte ID No 1351608CD1 1 Met Glu Ile Ser Ala Glu Leu Pro Gln Thr Pro Gln Arg Leu Ala 1 5 10 15 Ser Trp Trp Asp Gln Gln Val Asp Phe Tyr Thr Ala Phe Leu His 20 25 30 His Leu Ala Gln Leu Val Pro Glu Ile Tyr Phe Ala Glu Met Asp 35 40 45 Pro Asp Leu Glu Lys Gln Glu Glu Ser Val Gln Met Ser Ile Phe 50 55 60 Thr Pro Leu Glu Trp Tyr Leu Phe Gly Glu Asp Pro Asp Ile Cys 65 70 75 Leu Glu Lys Leu Lys His Ser Gly Ala Phe Gln Leu Cys Gly Arg 80 85 90 Val Phe Lys Ser Gly Glu Thr Thr Tyr Ser Cys Arg Asp Cys Ala 95 100 105 Ile Asp Pro Thr Cys Val Leu Cys Met Asp Cys Phe Gln Asp Ser 110 115 120 Val His Lys Asn His Arg Tyr Lys Met His Thr Ser Thr Gly Gly 125 130 135 Gly Phe Cys Asp Cys Gly Asp Thr Glu Ala Trp Lys Thr Gly Pro 140 145 150 Phe Cys Val Asn His Glu Pro Gly Arg Ala Gly Thr Ile Lys Glu 155 160 165 Asn Ser Arg Cys Pro Leu Asn Glu Glu Val Ile Val Gln Ala Arg 170 175 180 Lys Ile Phe Pro Ser Val Ile Lys Tyr Val Val Glu Met Thr Ile 185 190 195 Trp Glu Glu Glu Lys Glu Leu Pro Pro Glu Leu Gln Ile Arg Glu 200 205 210 Lys Asn Glu Arg Tyr Tyr Cys Val Leu Phe Asn Asp Glu His His 215 220 225 Ser Tyr Asp His Val Ile Tyr Ser Leu Gln Arg Ala Leu Asp Cys 230 235 240 Glu Leu Ala Glu Ala Gln Leu His Thr Thr Ala Ile Asp Lys Glu 245 250 255 Gly Arg Arg Ala Val Lys Ala Gly Ala Tyr Ala Ala Cys Gln Glu 260 265 270 Ala Lys Glu Asp Ile Lys Ser His Ser Glu Asn Val Ser Gln His 275 280 285 Pro Leu His Val Glu Val Leu His Ser Glu Ile Met Ala His Gln 290 295 300 Lys Phe Ala Leu Arg Leu Gly Ser Trp Met Asn Lys Ile Met Ser 305 310 315 Tyr Ser Ser Asp Phe Arg Gln Ile Phe Cys Gln Ala Cys Leu Arg 320 325 330 Glu Glu Pro Asp Ser Glu Asn Pro Cys Leu Ile Ser Arg Leu Met 335 340 345 Leu Trp Asp Ala Lys Leu Tyr Lys Gly Ala Arg Lys Ile Leu His 350 355 360 Glu Leu Ile Phe Ser Ser Phe Phe Met Glu Met Glu Tyr Lys Lys 365 370 375 Leu Phe Ala Met Glu Phe Val Lys Tyr Tyr Lys Gln Leu Gln Lys 380 385 390 Glu Tyr Ile Ser Asp Asp His Asp Arg Ser Ile Ser Ile Thr Ala 395 400 405 Leu Ser Val Gln Met Phe Thr Val Pro Thr Leu Ala Arg His Leu 410 415 420 Ile Glu Glu Gln Asn Val Ile Ser Val Ile Thr Glu Thr Leu Leu 425 430 435 Glu Val Leu Pro Glu Tyr Leu Asp Arg Asn Asn Lys Phe Asn Phe 440 445 450 Gln Gly Tyr Ser Gln Asp Lys Leu Gly Arg Val Tyr Ala Val Ile 455 460 465 Cys Asp Leu Lys Tyr Ile Leu Ile Ser Lys Pro Thr Ile Trp Thr 470 475 480 Glu Arg Leu Arg Met Gln Phe Leu Glu Gly Phe Arg Ser Phe Leu 485 490 495 Lys Ile Leu Thr Cys Met Gln Gly Met Glu Glu Ile Arg Arg Gln 500 505 510 Val Gly Gln His Ile Glu Val Asp Pro Asp Trp Glu Ala Ala Ile 515 520 525 Ala Ile Gln Met Gln Leu Lys Asn Ile Leu Leu Met Phe Gln Glu 530 535 540 Trp Cys Ala Cys Asp Glu Glu Leu Leu Leu Val Ala Tyr Lys Glu 545 550 555 Cys His Lys Ala Val Met Arg Cys Ser Thr Ser Phe Ile Ser Ser 560 565 570 Ser Lys Thr Val Val Gln Ser Cys Gly His Ser Leu Glu Thr Lys 575 580 585 Ser Tyr Arg Val Ser Glu Asp Leu Val Ser Ile His Leu Pro Leu 590 595 600 Ser Arg Thr Leu Ala Gly Leu His Val Arg Leu Ser Arg Leu Gly 605 610 615 Ala Val Ser Arg Leu His Glu Phe Val Ser Phe Glu Asp Phe Gln 620 625 630 Val Glu Val Leu Val Glu Tyr Pro Leu Arg Cys Leu Val Leu Val 635 640 645 Ala Gln Val Val Ala Glu Met Trp Arg Arg Asn Gly Leu Ser Leu 650 655 660 Ile Ser Gln Val Phe Tyr Tyr Gln Asp Val Lys Cys Arg Glu Glu 665 670 675 Met Tyr Asp Lys Asp Ile Ile Met Leu Gln Ile Gly Ala Ser Leu 680 685 690 Met Asp Pro Asn Lys Phe Leu Leu Leu Val Leu Gln Arg Tyr Glu 695 700 705 Leu Ala Glu Ala Phe Asn Lys Thr Ile Ser Thr Lys Asp Gln Asp 710 715 720 Leu Ile Lys Gln Tyr Asn Thr Leu Ile Glu Glu Met Leu Gln Val 725 730 735 Leu Ile Tyr Ile Val Gly Glu Arg Tyr Val Pro Gly Val Gly Asn 740 745 750 Val Thr Lys Glu Glu Val Thr Met Arg Glu Ile Ile His Leu Leu 755 760 765 Cys Ile Glu Pro Met Pro His Ser Ala Ile Ala Lys Asn Leu Pro 770 775 780 Glu Asn Glu Asn Asn Glu Thr Gly Leu Glu Asn Val Ile Asn Lys 785 790 795 Val Ala Thr Phe Lys Lys Pro Gly Val Ser Gly His Gly Val Tyr 800 805 810 Glu Leu Lys Asp Glu Ser Leu Lys Asp Phe Asn Met Tyr Phe Tyr 815 820 825 His Tyr Ser Lys Thr Gln His Ser Lys Ala Glu His Met Gln Lys 830 835 840 Lys Arg Arg Lys Gln Glu Asn Lys Asp Glu Ala Leu Pro Pro Pro 845 850 855 Pro Pro Pro Glu Phe Cys Pro Ala Phe Ser Lys Val Ile Asn Leu 860 865 870 Leu Asn Cys Asp Ile Met Met Tyr Ile Leu Arg Thr Val Phe Glu 875 880 885 Arg Ala Ile Asp Thr Asp Ser Asn Leu Trp Thr Glu Gly Met Leu 890 895 900 Gln Met Ala Phe His Ile Leu Ala Leu Gly Leu Leu Glu Glu Lys 905 910 915 Gln Gln Leu Gln Lys Ala Pro Glu Glu Glu Val Thr Phe Asp Phe 920 925 930 Tyr His Lys Ala Ser Arg Leu Gly Ser Ser Ala Met Asn Ile Gln 935 940 945 Met Leu Leu Glu Lys Leu Lys Gly Ile Pro Gln Leu Glu Gly Gln 950 955 960 Lys Asp Met Ile Thr Trp Ile Leu Gln Met Phe Asp Thr Val Lys 965 970 975 Arg Leu Arg Glu Lys Ser Cys Leu Ile Val Ala Thr Thr Ser Gly 980 985 990 Ser Glu Ser Ile Lys Asn Asp Glu Ile Thr His Asp Lys Glu Lys 995 1000 1005 Ala Glu Arg Lys Arg Lys Ala Glu Ala Ala Arg Leu His Arg Gln 1010 1015 1020 Lys Ile Met Ala Gln Met Ser Ala Leu Gln Lys Asn Phe Ile Glu 1025 1030 1035 Thr His Lys Leu Met Tyr Asp Asn Thr Ser Glu Met Pro Gly Lys 1040 1045 1050 Glu Asp Ser Ile Met Glu Glu Glu Ser Thr Pro Ala Val Ser Asp 1055 1060 1065 Tyr Ser Arg Ile Ala Leu Gly Pro Lys Arg Gly Pro Ser Val Thr 1070 1075 1080 Glu Lys Glu Val Leu Thr Cys Ile Leu Cys Gln Glu Glu Gln Glu 1085 1090 1095 Val Lys Ile Glu Asn Asn Ala Met Val Leu Ser Ala Cys Val Gln 1100 1105 1110 Lys Ser Thr Ala Leu Thr Gln His Arg Gly Lys Pro Ile Glu Leu 1115 1120 1125 Ser Gly Glu Ala Leu Asp Pro Leu Phe Met Asp Pro Asp Leu Ala 1130 1135 1140 Tyr Gly Thr Tyr Thr Gly Ser Cys Gly His Val Met His Ala Val 1145 1150 1155 Cys Trp Gln Lys Tyr Phe Glu Ala Val Gln Leu Ser Ser Gln Gln 1160 1165 1170 Arg Ile His Val Asp Leu Phe Asp Leu Glu Ser Gly Glu Tyr Leu 1175 1180 1185 Cys Pro Leu Cys Lys Ser Leu Cys Asn Thr Val Ile Pro Ile Ile 1190 1195 1200 Pro Leu Gln Pro Gln Lys Ile Asn Ser Glu Asn Ala Asp Ala Leu 1205 1210 1215 Ala Gln Leu Leu Thr Leu Ala Arg Trp Ile Gln Thr Val Leu Ala 1220 1225 1230 Arg Ile Ser Gly Tyr Asn Ile Arg His Ala Lys Gly Glu Asn Pro 1235 1240 1245 Ile Pro Ile Phe Phe Asn Gln Gly Met Gly Asp Ser Thr Leu Glu 1250 1255 1260 Phe His Ser Ile Leu Ser Phe Gly Val Glu Ser Ser Ile Lys Tyr 1265 1270 1275 Ser Asn Ser Ile Lys Glu Met Val Ile Leu Phe Ala Thr Thr Ile 1280 1285 1290 Tyr Arg Ile Gly Leu Lys Val Pro Pro Asp Glu Arg Asp Pro Arg 1295 1300 1305 Val Pro Met Leu Thr Trp Ser Thr Cys Ala Phe Thr Ile Gln Ala 1310 1315 1320 Ile Glu Asn Leu Leu Gly Asp Glu Gly Lys Pro Leu Phe Gly Ala 1325 1330 1335 Leu Gln Asn Arg Gln His Asn Gly Leu Lys Ala Leu Met Gln Phe 1340 1345 1350 Ala Val Ala Gln Arg Ile Thr Cys Pro Gln Val Leu Ile Gln Lys 1355 1360 1365 His Leu Val Arg Leu Leu Ser Val Val Leu Pro Asn Ile Lys Ser 1370 1375 1380 Glu Asp Thr Pro Cys Leu Leu Ser Ile Asp Leu Phe His Val Leu 1385 1390 1395 Val Gly Ala Val Leu Ala Phe Pro Ser Leu Tyr Trp Asp Asp Pro 1400 1405 1410 Val Asp Leu Gln Pro Ser Ser Val Ser Ser Ser Tyr Asn His Leu 1415 1420 1425 Tyr Leu Phe His Leu Ile Thr Met Ala His Met Leu Gln Ile Leu 1430 1435 1440 Leu Thr Val Asp Thr Gly Leu Pro Leu Ala Gln Val Gln Glu Asp 1445 1450 1455 Ser Glu Glu Ala His Ser Ala Ser Ser Phe Phe Ala Glu Ile Ser 1460 1465 1470 Gln Tyr Thr Ser Gly Ser Ile Gly Cys Asp Ile Pro Gly Trp Tyr 1475 1480 1485 Leu Trp Val Ser Leu Lys Asn Gly Ile Thr Pro Tyr Leu Arg Cys 1490 1495 1500 Ala Ala Leu Phe Phe His Tyr Leu Leu Gly Val Thr Pro Pro Glu 1505 1510 1515 Glu Leu His Thr Asn Ser Ala Glu Gly Glu Tyr Ser Ala Leu Cys 1520 1525 1530 Ser Tyr Leu Ser Leu Pro Thr Asn Leu Phe Leu Leu Phe Gln Glu 1535 1540 1545 Tyr Trp Asp Thr Val Arg Pro Leu Leu Gln Arg Trp Cys Ala Asp 1550 1555 1560 Pro Ala Leu Leu Asn Cys Leu Lys Gln Lys Asn Thr Val Val Arg 1565 1570 1575 Tyr Pro Arg Lys Arg Asn Ser Leu Ile Glu Leu Pro Asp Asp Tyr 1580 1585 1590 Ser Cys Leu Leu Asn Gln Ala Ser His Phe Arg Cys Pro Arg Ser 1595 1600 1605 Ala Asp Asp Glu Arg Lys His Pro Val Leu Cys Leu Phe Cys Gly 1610 1615 1620 Ala Ile Leu Cys Ser Gln Asn Ile Cys Cys Gln Glu Ile Val Asn 1625 1630 1635 Gly Glu Glu Val Gly Ala Cys Ile Phe His Ala Leu His Cys Gly 1640 1645 1650 Ala Gly Val Cys Ile Phe Leu Lys Ile Arg Glu Cys Arg Val Val 1655 1660 1665 Leu Val Glu Gly Lys Ala Arg Gly Cys Ala Tyr Pro Ala Pro Tyr 1670 1675 1680 Leu Asp Glu Tyr Gly Glu Thr Asp Pro Gly Leu Lys Arg Gly Asn 1685 1690 1695 Pro Leu His Leu Ser Arg Glu Arg Tyr Arg Lys Leu His Leu Val 1700 1705 1710 Trp Gln Gln His Cys Ile Ile Glu Glu Ile Ala Arg Ser Gln Glu 1715 1720 1725 Thr Asn Gln Met Leu Phe Gly Phe Asn Trp Gln Leu Leu 1730 1735 2 389 PRT Homo sapiens misc_feature Incyte ID No 4259314CD1 2 Met Glu Gly Ser Glu Pro Val Ala Ala His Gln Gly Glu Glu Ala 1 5 10 15 Ser Cys Ser Ser Trp Gly Thr Gly Ser Thr Asn Lys Asn Leu Pro 20 25 30 Ile Met Ser Thr Ala Ser Val Glu Ile Asp Asp Ala Leu Tyr Ser 35 40 45 Arg Gln Arg Tyr Val Leu Gly Asp Thr Ala Met Gln Lys Met Ala 50 55 60 Lys Ser His Val Phe Leu Ser Gly Met Gly Gly Leu Gly Leu Glu 65 70 75 Ile Ala Lys Asn Leu Val Leu Ala Gly Ile Lys Ala Val Thr Ile 80 85 90 His Asp Thr Glu Lys Cys Gln Ala Trp Asp Leu Gly Thr Asn Phe 95 100 105 Phe Leu Ser Glu Asp Asp Val Val Asn Lys Arg Asn Arg Ala Glu 110 115 120 Ala Val Leu Lys His Ile Ala Glu Leu Asn Pro Tyr Val His Val 125 130 135 Thr Ser Ser Ser Val Pro Phe Asn Glu Thr Thr Asp Leu Ser Phe 140 145 150 Leu Asp Lys Tyr Gln Cys Val Val Leu Thr Glu Met Lys Leu Pro 155 160 165 Leu Gln Lys Lys Ile Asn Asp Phe Cys Arg Ser Gln Cys Pro Pro 170 175 180 Ile Lys Phe Ile Ser Ala Asp Val His Gly Ile Trp Ser Arg Leu 185 190 195 Phe Cys Asp Phe Gly Asp Glu Phe Glu Val Leu Asp Thr Thr Gly 200 205 210 Glu Glu Pro Lys Glu Ile Phe Ile Ser Asn Ile Thr Gln Ala Asn 215 220 225 Pro Gly Ile Val Thr Cys Leu Glu Asn His Pro His Lys Leu Glu 230 235 240 Thr Gly Gln Phe Leu Thr Phe Arg Glu Ile Asn Gly Met Thr Gly 245 250 255 Leu Asn Gly Ser Ile Gln Gln Ile Thr Val Ile Ser Pro Phe Ser 260 265 270 Phe Ser Ile Gly Asp Thr Thr Glu Leu Glu Pro Tyr Leu His Gly 275 280 285 Gly Ile Ala Val Gln Val Lys Thr Pro Lys Thr Val Phe Phe Glu 290 295 300 Ser Leu Glu Arg Gln Leu Lys His Pro Lys Cys Leu Ile Val Asp 305 310 315 Phe Ser Asn Pro Glu Ala Pro Leu Glu Ile His Thr Ala Met Leu 320 325 330 Ala Leu Asp Gln Phe Gln Glu Lys Tyr Ser Arg Lys Pro Asn Val 335 340 345 Gly Cys Gln Gln Asp Ser Glu Glu Leu Leu Lys Leu Ala Thr Ser 350 355 360 Ile Ser Glu Thr Leu Glu Glu Lys Val Thr Ile Glu Ile Tyr Gly 365 370 375 Cys Pro Asn Ile Cys Leu Leu Ile His Lys Cys Ser Val Tyr 380 385 3 854 PRT Homo sapiens misc_feature Incyte ID No 3660046CD1 3 Met Glu Arg Pro Tyr Thr Phe Lys Asp Phe Leu Leu Arg Pro Arg 1 5 10 15 Ser His Lys Ser Arg Val Lys Gly Phe Leu Arg Leu Lys Met Ala 20 25 30 Tyr Met Pro Lys Asn Gly Gly Gln Asp Glu Glu Asn Ser Asp Gln 35 40 45 Arg Asp Asp Met Glu His Gly Trp Glu Val Val Asp Ser Asn Asp 50 55 60 Ser Ala Ser Gln His Gln Glu Glu Leu Pro Pro Pro Pro Leu Pro 65 70 75 Pro Gly Trp Glu Glu Lys Val Asp Asn Leu Gly Arg Thr Tyr Tyr 80 85 90 Val Asn His Asn Asn Arg Thr Thr Gln Trp His Arg Pro Ser Leu 95 100 105 Met Asp Val Ser Ser Glu Ser Asp Asn Asn Ile Arg Gln Ile Asn 110 115 120 Gln Glu Ala Ala His Arg Arg Phe Arg Ser Arg Arg His Ile Ser 125 130 135 Glu Asp Leu Glu Pro Glu Pro Ser Glu Gly Gly Asp Val Pro Glu 140 145 150 Pro Trp Glu Thr Ile Ser Glu Glu Val Asn Ile Ala Gly Asp Ser 155 160 165 Leu Gly Leu Ala Leu Pro Pro Pro Pro Ala Ser Pro Gly Ser Arg 170 175 180 Thr Ser Pro Gln Glu Leu Ser Glu Glu Leu Ser Arg Arg Leu Gln 185 190 195 Ile Thr Pro Asp Ser Asn Gly Glu Gln Phe Ser Ser Leu Ile Gln 200 205 210 Arg Glu Pro Ser Ser Arg Leu Arg Ser Cys Ser Val Thr Asp Ala 215 220 225 Val Ala Glu Gln Gly His Leu Pro Pro Pro Ser Ala Pro Ala Gly 230 235 240 Arg Ala Arg Ser Ser Thr Val Thr Gly Gly Glu Glu Pro Thr Pro 245 250 255 Ser Val Ala Tyr Val His Thr Thr Pro Gly Leu Pro Ser Gly Trp 260 265 270 Glu Glu Arg Lys Asp Ala Lys Gly Arg Thr Tyr Tyr Val Asn His 275 280 285 Asn Asn Arg Thr Thr Thr Trp Thr Arg Pro Ile Met Gln Leu Ala 290 295 300 Glu Asp Gly Ala Ser Gly Ser Ala Thr Asn Ser Asn Asn His Leu 305 310 315 Ile Glu Pro Gln Ile Arg Arg Pro Arg Ser Leu Ser Ser Pro Thr 320 325 330 Val Thr Leu Ser Ala Pro Leu Glu Gly Ala Lys Asp Ser Pro Val 335 340 345 Arg Arg Ala Val Lys Asp Thr Leu Ser Asn Pro Gln Ser Pro Gln 350 355 360 Pro Ser Pro Tyr Asn Ser Pro Lys Pro Gln His Lys Val Thr Gln 365 370 375 Ser Phe Leu Pro Pro Gly Trp Glu Met Arg Ile Ala Pro Asn Gly 380 385 390 Arg Pro Phe Phe Ile Asp His Asn Thr Lys Thr Thr Thr Trp Glu 395 400 405 Asp Pro Arg Leu Lys Phe Pro Val His Met Arg Ser Lys Thr Ser 410 415 420 Leu Asn Pro Asn Asp Leu Gly Pro Leu Pro Pro Gly Trp Glu Glu 425 430 435 Arg Thr His Thr Asp Gly Arg Ile Phe Tyr Ile Asn His Asn Ile 440 445 450 Lys Arg Thr Gln Trp Glu Asp Pro Arg Leu Glu Asn Val Ala Ile 455 460 465 Thr Gly Pro Ala Val Pro Tyr Ser Arg Asp Tyr Lys Arg Lys Tyr 470 475 480 Glu Phe Phe Arg Arg Lys Leu Lys Lys Gln Asn Asp Ile Pro Asn 485 490 495 Lys Phe Glu Met Lys Leu Arg Arg Ala Thr Val Leu Glu Asp Ser 500 505 510 Tyr Arg Arg Ile Met Gly Val Lys Arg Ala Asp Phe Leu Lys Ala 515 520 525 Arg Leu Trp Ile Glu Phe Asp Gly Glu Lys Gly Leu Asp Tyr Gly 530 535 540 Gly Val Ala Arg Glu Trp Phe Phe Leu Ile Ser Lys Glu Met Phe 545 550 555 Asn Pro Tyr Tyr Gly Leu Phe Glu Tyr Ser Ala Thr Asp Asn Tyr 560 565 570 Thr Leu Gln Ile Asn Pro Asn Ser Gly Leu Cys Asn Glu Asp His 575 580 585 Leu Ser Tyr Phe Lys Phe Ile Gly Arg Val Ala Gly Met Ala Val 590 595 600 Tyr His Gly Lys Leu Leu Asp Gly Phe Phe Ile Arg Pro Phe Tyr 605 610 615 Lys Met Met Leu His Lys Pro Ile Thr Leu His Asp Met Glu Ser 620 625 630 Val Asp Ser Glu Tyr Tyr Asn Ser Leu Arg Trp Ile Leu Glu Asn 635 640 645 Asp Pro Thr Glu Leu Asp Leu Arg Phe Ile Ile Asp Glu Glu Leu 650 655 660 Phe Gly Gln Thr His Gln His Glu Leu Lys Asn Gly Gly Ser Glu 665 670 675 Ile Val Val Thr Asn Lys Asn Lys Lys Glu Tyr Ile Tyr Leu Val 680 685 690 Ile Gln Trp Arg Phe Val Asn Arg Ile Gln Lys Gln Met Ala Ala 695 700 705 Phe Lys Glu Gly Phe Phe Glu Leu Ile Pro Gln Asp Leu Ile Lys 710 715 720 Ile Phe Asp Glu Asn Glu Leu Glu Leu Leu Met Cys Gly Leu Gly 725 730 735 Asp Val Asp Val Asn Asp Trp Arg Glu His Thr Lys Tyr Lys Asn 740 745 750 Gly Tyr Ser Ala Asn His Gln Val Ile Gln Trp Phe Trp Lys Ala 755 760 765 Val Leu Met Met Asp Ser Glu Lys Arg Ile Arg Leu Leu Gln Phe 770 775 780 Val Thr Gly Thr Ser Arg Val Pro Met Asn Gly Phe Ala Glu Leu 785 790 795 Tyr Gly Ser Asn Gly Pro Gln Ser Phe Thr Val Glu Gln Trp Gly 800 805 810 Thr Pro Glu Lys Leu Pro Arg Ala His Thr Cys Phe Asn Arg Leu 815 820 825 Asp Leu Pro Pro Tyr Glu Ser Phe Glu Glu Leu Trp Asp Lys Leu 830 835 840 Gln Met Ala Ile Glu Asn Thr Gln Gly Phe Asp Gly Val Asp 845 850 4 111 PRT Homo sapiens misc_feature Incyte ID No 3016416CD1 4 Met Val Ser Leu Trp Val Glu Asp Thr Phe Leu Ser Pro Gly Phe 1 5 10 15 Gly Phe Ala His Val Ala Cys Ser Gly Leu Gly Met Lys Gln Lys 20 25 30 Arg Lys Ala Ala Ser Ser Glu Pro Thr Ser Glu Val Ala Leu Gly 35 40 45 Gly Ser Ala Gly Pro Val Arg Ser His Leu His Pro Glu Gly Leu 50 55 60 Leu Trp Cys Ser Arg Cys Phe Phe Ser Leu Arg Pro Lys Gly Thr 65 70 75 Glu Pro Pro Gly Arg Ser Ala Gly Leu Gln Gly Ala Thr Glu Arg 80 85 90 Ser Gly Trp Thr Ser Val Gln Ala Gln Ala Gln Ala Cys Glu Asn 95 100 105 Leu Val Pro Ala Ala Val 110 5 538 PRT Homo sapiens misc_feature Incyte ID No 2133755CD1 5 Met Trp Ser Gly Arg Ser Ser Phe Thr Ser Leu Val Val Gly Val 1 5 10 15 Phe Val Val Tyr Val Val His Thr Cys Trp Val Met Tyr Gly Ile 20 25 30 Val Tyr Thr Arg Pro Cys Ser Gly Asp Ala Asn Cys Ile Gln Pro 35 40 45 Tyr Leu Ala Arg Arg Pro Lys Leu Gln Leu Ser Val Tyr Thr Thr 50 55 60 Thr Arg Ser His Leu Gly Ala Glu Asn Asn Ile Asp Leu Val Leu 65 70 75 Asn Val Glu Asp Phe Asp Val Glu Ser Lys Phe Glu Arg Thr Val 80 85 90 Asn Val Ser Val Pro Lys Lys Thr Arg Asn Asn Gly Thr Leu Tyr 95 100 105 Ala Tyr Ile Phe Leu His His Ala Gly Val Leu Pro Trp His Asp 110 115 120 Gly Lys Gln Val His Leu Val Ser Pro Leu Thr Thr Tyr Met Val 125 130 135 Pro Lys Pro Glu Glu Ile Asn Leu Leu Thr Gly Glu Ser Asp Thr 140 145 150 Gln Gln Ile Glu Ala Glu Lys Lys Pro Thr Ser Ala Leu Asp Glu 155 160 165 Pro Val Ser His Trp Arg Pro Arg Leu Ala Leu Asn Val Met Ala 170 175 180 Asp Asn Phe Val Phe Asp Gly Ser Ser Leu Pro Ala Asp Val His 185 190 195 Arg Tyr Met Lys Met Ile Gln Leu Gly Lys Thr Val His Tyr Leu 200 205 210 Pro Ile Leu Phe Ile Asp Gln Leu Ser Asn Arg Val Lys Asp Leu 215 220 225 Met Val Ile Asn Arg Ser Thr Thr Glu Leu Pro Leu Thr Val Ser 230 235 240 Tyr Asp Lys Val Ser Leu Gly Arg Leu Arg Phe Trp Ile His Met 245 250 255 Gln Asp Ala Val Tyr Ser Leu Gln Gln Phe Gly Phe Ser Glu Lys 260 265 270 Asp Ala Asp Glu Val Lys Gly Ile Phe Val Asp Thr Asn Leu Tyr 275 280 285 Phe Leu Ala Leu Thr Phe Phe Val Ala Ala Phe His Leu Leu Phe 290 295 300 Asp Phe Leu Ala Phe Lys Asn Asp Ile Ser Phe Trp Lys Lys Lys 305 310 315 Lys Ser Met Ile Gly Met Ser Thr Lys Ala Val Leu Trp Arg Cys 320 325 330 Phe Ser Thr Val Val Ile Phe Leu Phe Leu Leu Asp Glu Gln Thr 335 340 345 Ser Leu Leu Val Leu Val Pro Ala Gly Val Gly Ala Ala Ile Glu 350 355 360 Leu Trp Lys Val Lys Lys Ala Leu Lys Met Thr Ile Phe Trp Arg 365 370 375 Gly Leu Met Pro Glu Phe Gln Phe Gly Thr Tyr Ser Glu Ser Glu 380 385 390 Arg Lys Thr Glu Glu Tyr Asp Thr Gln Ala Met Lys Tyr Leu Ser 395 400 405 Tyr Leu Leu Tyr Pro Leu Cys Val Gly Gly Ala Val Tyr Ser Leu 410 415 420 Leu Asn Ile Lys Tyr Lys Ser Trp Tyr Ser Trp Leu Ile Asn Ser 425 430 435 Phe Val Asn Gly Val Tyr Ala Phe Gly Phe Leu Phe Met Leu Pro 440 445 450 Gln Leu Phe Val Asn Tyr Lys Leu Lys Ser Val Ala His Leu Pro 455 460 465 Trp Lys Ala Phe Thr Tyr Lys Ala Phe Asn Thr Phe Ile Asp Asp 470 475 480 Val Phe Ala Phe Ile Ile Thr Met Pro Thr Ser His Arg Leu Ala 485 490 495 Cys Phe Arg Asp Asp Val Val Phe Leu Val Tyr Leu Tyr Gln Arg 500 505 510 Trp Leu Tyr Pro Val Asp Lys Arg Arg Val Asn Glu Phe Gly Glu 515 520 525 Ser Tyr Glu Glu Lys Ala Thr Arg Ala Pro His Thr Asp 530 535 6 474 PRT Homo sapiens misc_feature Incyte ID No 5259957CD1 6 Met Ser Ile Arg Ala Pro Pro Arg Leu Leu Glu Leu Ala Arg Gln 1 5 10 15 Arg Leu Leu Arg Asp Gln Ala Leu Ala Ile Ser Thr Met Glu Glu 20 25 30 Leu Pro Arg Glu Leu Phe Pro Thr Leu Phe Met Glu Ala Phe Ser 35 40 45 Arg Arg Arg Cys Glu Thr Leu Lys Thr Met Val Gln Ala Trp Pro 50 55 60 Phe Thr Arg Leu Pro Leu Gly Ser Leu Met Lys Ser Pro His Leu 65 70 75 Glu Ser Leu Lys Ser Val Leu Glu Gly Val Asp Val Leu Leu Thr 80 85 90 Gln Glu Val Arg Pro Arg Gln Ser Lys Leu Gln Val Leu Asp Leu 95 100 105 Arg Asn Val Asp Glu Asn Phe Cys Asp Ile Phe Ser Gly Ala Thr 110 115 120 Ala Ser Phe Pro Glu Ala Leu Ser Gln Lys Gln Thr Ala Asp Asn 125 130 135 Cys Pro Gly Thr Gly Arg Gln Gln Pro Phe Met Val Phe Ile Asp 140 145 150 Leu Cys Leu Lys Asn Arg Thr Leu Asp Glu Cys Leu Thr His Leu 155 160 165 Leu Glu Trp Gly Lys Gln Arg Lys Gly Leu Leu His Val Cys Cys 170 175 180 Lys Glu Leu Gln Val Phe Gly Met Pro Ile His Ser Ile Ile Glu 185 190 195 Val Leu Asn Met Val Glu Leu Asp Cys Ile Gln Glu Val Glu Val 200 205 210 Cys Cys Pro Trp Glu Leu Ser Thr Leu Val Lys Phe Ala Pro Tyr 215 220 225 Leu Gly Gln Met Arg Asn Leu Arg Lys Leu Val Leu Phe Asn Ile 230 235 240 Arg Ala Ser Ala Cys Ile Pro Pro Asp Asn Lys Gly Gln Phe Ile 245 250 255 Ala Arg Phe Thr Ser Gln Phe Leu Lys Leu Asp Tyr Phe Gln Asn 260 265 270 Leu Ser Met His Ser Val Ser Phe Leu Glu Gly His Leu Asp Gln 275 280 285 Leu Leu Arg Cys Leu Gln Ala Ser Leu Glu Met Val Val Met Thr 290 295 300 Asp Cys Leu Leu Ser Glu Ser Asp Leu Lys His Leu Ser Trp Cys 305 310 315 Pro Ser Ile Arg Gln Leu Lys Glu Leu Asp Leu Arg Gly Val Thr 320 325 330 Leu Thr His Phe Ser Pro Glu Pro Leu Thr Gly Leu Leu Glu Gln 335 340 345 Ala Val Ala Thr Leu Gln Thr Leu Asp Leu Glu Asp Cys Gly Ile 350 355 360 Met Asp Ser Gln Leu Ser Ala Ile Leu Pro Val Leu Ser Arg Cys 365 370 375 Ser Gln Leu Ser Thr Phe Ser Phe Cys Gly Asn Leu Ile Ser Met 380 385 390 Ala Ala Leu Glu Asn Leu Leu Arg His Thr Val Gly Leu Ser Lys 395 400 405 Leu Ser Leu Glu Leu Tyr Pro Ala Pro Leu Glu Ser Tyr Asp Thr 410 415 420 Gln Gly Ala Leu Cys Trp Gly Arg Phe Ala Glu Leu Gly Ala Glu 425 430 435 Leu Met Asn Thr Leu Arg Asp Leu Arg Gln Pro Lys Ile Ile Val 440 445 450 Phe Cys Thr Val Pro Cys Pro Arg Cys Gly Ile Arg Ala Ser Tyr 455 460 465 Asp Leu Glu Pro Ser His Cys Leu Cys 470 7 354 PRT Homo sapiens misc_feature Incyte ID No 55029783CD1 7 Met Pro Leu Leu Gly Gln Thr Val Arg Ser Ala Ser Ala Arg Thr 1 5 10 15 Arg Arg Trp Ser Arg Arg Ala Ala Gly Asp Arg Pro Gly Ala Pro 20 25 30 Ser Glu Ala Arg Arg Pro Gln Leu Arg Gly Asp His Gly Ile Leu 35 40 45 Val Asp Arg Val Arg Gly His Trp Arg Ile Ala Ala Gly Ser Cys 50 55 60 Ser Thr Cys Trp Cys Pro Ser Ala Leu Cys Ser Ser Thr Asn Gly 65 70 75 Phe Met Cys Thr Thr Gly Phe Pro Asn Met Ser Leu Thr Leu Val 80 85 90 His Phe Val Val Thr Trp Leu Gly Leu Tyr Ile Cys Gln Lys Leu 95 100 105 Asp Ile Phe Ala Pro Lys Ser Leu Pro Pro Ser Arg Leu Leu Leu 110 115 120 Leu Ala Leu Ser Phe Cys Gly Phe Val Val Phe Thr Asn Leu Ser 125 130 135 Leu Gln Asn Asn Thr Ile Gly Thr Tyr Gln Leu Ala Lys Ala Met 140 145 150 Thr Thr Pro Val Ile Ile Ala Ile Gln Thr Phe Cys Tyr Gln Lys 155 160 165 Thr Phe Ser Thr Arg Ile Gln Leu Thr Leu Ile Pro Ile Thr Leu 170 175 180 Gly Val Ile Leu Asn Ser Tyr Tyr Asp Val Lys Phe Asn Phe Leu 185 190 195 Gly Met Val Phe Ala Ala Leu Gly Val Leu Val Thr Ser Leu Tyr 200 205 210 Gln Val Trp Val Gly Ala Lys Gln His Glu Leu Gln Val Asn Ser 215 220 225 Met Gln Leu Leu Tyr Tyr Gln Ala Pro Met Ser Ser Ala Met Leu 230 235 240 Leu Val Ala Val Pro Phe Phe Glu Pro Val Phe Gly Glu Gly Gly 245 250 255 Ile Phe Gly Pro Trp Ser Val Ser Ala Leu Leu Met Val Leu Leu 260 265 270 Ser Gly Val Ile Ala Phe Met Val Asn Leu Ser Ile Tyr Trp Ile 275 280 285 Ile Gly Asn Thr Ser Pro Val Thr Tyr Asn Met Phe Gly His Phe 290 295 300 Lys Phe Cys Ile Thr Leu Phe Gly Gly Tyr Val Leu Phe Lys Asp 305 310 315 Pro Leu Ser Ile Asn Gln Ala Leu Gly Ile Leu Cys Thr Leu Phe 320 325 330 Gly Ile Leu Ala Tyr Thr His Phe Lys Leu Ser Glu Gln Glu Gly 335 340 345 Ser Arg Ser Lys Leu Ala Gln Arg Pro 350 8 272 PRT Homo sapiens misc_feature Incyte ID No 8032202CD1 8 Met Met Cys Pro Leu Trp Arg Leu Leu Ile Phe Leu Gly Leu Leu 1 5 10 15 Ala Leu Pro Leu Ala Pro His Lys Gln Pro Trp Pro Gly Leu Ala 20 25 30 Gln Ala His Arg Asp Asn Lys Ser Thr Leu Ala Arg Ile Ile Ala 35 40 45 Gln Gly Leu Ile Lys His Asn Ala Glu Ser Arg Ile Gln Asn Ile 50 55 60 His Phe Gly Asp Arg Leu Asn Ala Ser Ala Gln Val Ala Pro Gly 65 70 75 Leu Val Gly Trp Leu Ile Ser Gly Arg Lys His Gln Gln Gln Gln 80 85 90 Glu Ser Ser Ile Asn Ile Thr Asn Ile Gln Leu Asp Cys Gly Gly 95 100 105 Ile Gln Ile Ser Phe His Lys Glu Trp Phe Ser Ala Asn Ile Ser 110 115 120 Leu Glu Phe Asp Leu Glu Leu Arg Pro Ser Phe Asp Asn Asn Ile 125 130 135 Val Lys Met Cys Ala His Met Ser Ile Val Val Glu Phe Trp Leu 140 145 150 Glu Lys Asp Glu Phe Gly Arg Arg Asp Leu Val Ile Gly Lys Cys 155 160 165 Asp Ala Glu Pro Ser Ser Val His Val Ala Ile Leu Thr Glu Ala 170 175 180 Ile Pro Pro Lys Met Asn Gln Phe Leu Tyr Asn Leu Lys Glu Asn 185 190 195 Leu Gln Lys Val Leu Pro His Met Val Glu Ser Gln Val Cys Pro 200 205 210 Leu Ile Gly Glu Ile Leu Gly Gln Leu Asp Val Lys Leu Leu Lys 215 220 225 Ser Leu Ile Glu Gln Glu Ala Ala His Glu Pro Thr His His Glu 230 235 240 Thr Ser Gln Pro Ser Cys Met Pro Gly Trp Arg Val Pro Gln Leu 245 250 255 Thr Ser Ala Asp Gln Lys Glu Ser Pro His Leu Ala Thr Leu Ser 260 265 270 Leu Pro 9 710 PRT Homo sapiens misc_feature Incyte ID No 6937367CD1 9 Met Glu Arg Thr Ala Gly Lys Glu Leu Ala Leu Ala Pro Leu Gln 1 5 10 15 Asp Trp Gly Glu Glu Thr Glu Asp Gly Ala Val Tyr Ser Val Ser 20 25 30 Leu Arg Arg Gln Arg Ser Gln Arg Arg Ser Pro Ala Glu Gly Pro 35 40 45 Gly Gly Ser Gln Ala Pro Ser Pro Ile Ala Asn Thr Phe Leu His 50 55 60 Tyr Arg Thr Ser Lys Val Arg Val Leu Arg Ala Ala Arg Leu Glu 65 70 75 Arg Leu Val Gly Glu Leu Val Phe Gly Asp Arg Glu Gln Asp Pro 80 85 90 Ser Phe Met Pro Ala Phe Leu Ala Thr Tyr Arg Thr Phe Val Pro 95 100 105 Thr Ala Cys Leu Leu Gly Phe Leu Leu Pro Pro Met Pro Pro Pro 110 115 120 Pro Pro Pro Gly Val Glu Ile Lys Lys Thr Ala Val Gln Asp Leu 125 130 135 Ser Phe Asn Lys Asn Leu Arg Ala Val Val Ser Val Leu Gly Ser 140 145 150 Trp Leu Gln Asp His Pro Gln Asp Phe Arg Asp His Pro Ala His 155 160 165 Ser Asp Leu Gly Ser Val Arg Thr Phe Leu Gly Trp Ala Ala Pro 170 175 180 Gly Ser Ala Glu Ala Gln Lys Ala Glu Lys Leu Leu Glu Asp Phe 185 190 195 Leu Glu Glu Ala Glu Arg Glu Gln Glu Glu Glu Pro Pro Gln Val 200 205 210 Trp Thr Gly Pro Pro Arg Val Ala Gln Thr Ser Asp Pro Asp Ser 215 220 225 Ser Glu Ala Cys Ala Glu Glu Glu Glu Gly Leu Met Pro Gln Gly 230 235 240 Pro Gln Leu Leu Asp Phe Ser Val Asp Glu Val Ala Glu Gln Leu 245 250 255 Thr Leu Ile Asp Leu Glu Leu Phe Ser Lys Val Arg Leu Tyr Glu 260 265 270 Cys Leu Gly Ser Val Trp Ser Gln Arg Asp Arg Pro Gly Ala Ala 275 280 285 Gly Ala Ser Pro Thr Val Arg Ala Thr Val Ala Gln Phe Asn Thr 290 295 300 Val Thr Gly Cys Val Leu Gly Ser Val Leu Gly Ala Pro Gly Leu 305 310 315 Ala Ala Pro Gln Arg Ala Gln Arg Leu Glu Lys Trp Ile Arg Ile 320 325 330 Ala Gln Arg Cys Arg Glu Leu Arg Asn Phe Ser Ser Leu Arg Ala 335 340 345 Ile Leu Ser Ala Leu Gln Ser Asn Pro Ile Tyr Arg Leu Lys Arg 350 355 360 Ser Trp Gly Ala Val Ser Arg Glu Pro Leu Ser Thr Phe Arg Lys 365 370 375 Leu Ser Gln Ile Phe Ser Asp Glu Asn Asn His Leu Ser Ser Arg 380 385 390 Glu Ile Leu Phe Gln Glu Glu Ala Thr Glu Gly Ser Gln Glu Glu 395 400 405 Asp Asn Thr Pro Gly Ser Leu Pro Ser Lys Pro Pro Pro Gly Pro 410 415 420 Val Pro Tyr Leu Gly Thr Phe Leu Thr Asp Leu Val Met Leu Asp 425 430 435 Thr Ala Leu Pro Asp Met Leu Glu Gly Asp Leu Ile Asn Phe Glu 440 445 450 Lys Arg Arg Lys Glu Trp Glu Ile Leu Ala Arg Ile Gln Gln Leu 455 460 465 Gln Arg Arg Cys Gln Ser Tyr Thr Leu Ser Pro His Pro Pro Ile 470 475 480 Leu Ala Ala Leu His Ala Gln Asn Gln Leu Thr Glu Glu Gln Ser 485 490 495 Tyr Arg Leu Ser Arg Val Ile Glu Pro Pro Ala Ala Ser Cys Pro 500 505 510 Ser Ser Pro Arg Ile Arg Arg Arg Ile Ser Leu Thr Lys Arg Leu 515 520 525 Ser Ala Lys Leu Ala Arg Glu Lys Ser Ser Ser Pro Ser Gly Ser 530 535 540 Pro Gly Asp Pro Ser Ser Pro Thr Ser Ser Val Ser Pro Gly Ser 545 550 555 Pro Pro Ser Ser Pro Arg Ser Arg Asp Ala Pro Ala Gly Ser Pro 560 565 570 Pro Ala Ser Pro Gly Pro Gln Gly Pro Ser Thr Lys Leu Pro Leu 575 580 585 Ser Leu Asp Leu Pro Ser Pro Arg Pro Phe Ala Leu Pro Leu Gly 590 595 600 Ser Pro Arg Ile Pro Leu Pro Ala Gln Gln Ser Ser Glu Ala Arg 605 610 615 Val Ile Arg Val Ser Ile Asp Asn Asp His Gly Asn Leu Tyr Arg 620 625 630 Ser Ile Leu Leu Thr Ser Gln Asp Lys Ala Pro Ser Val Val Arg 635 640 645 Arg Ala Leu Gln Lys His Asn Val Pro Gln Pro Trp Ala Cys Asp 650 655 660 Tyr Gln Leu Phe Gln Val Leu Pro Gly Asp Arg Val Leu Leu Ile 665 670 675 Pro Asp Asn Ala Asn Val Phe Tyr Ala Met Ser Pro Val Ala Pro 680 685 690 Arg Asp Phe Met Leu Arg Arg Lys Glu Gly Thr Arg Asn Thr Leu 695 700 705 Ser Val Ser Pro Ser 710 10 490 PRT Homo sapiens misc_feature Incyte ID No 3876510CD1 10 Met Thr Ile Gly Arg Met Glu Asn Val Glu Val Phe Thr Ala Glu 1 5 10 15 Gly Lys Gly Arg Gly Leu Lys Ala Thr Lys Glu Phe Trp Ala Ala 20 25 30 Asp Ile Ile Phe Ala Glu Arg Ala Tyr Ser Ala Val Val Phe Asp 35 40 45 Ser Leu Val Asn Phe Val Cys His Thr Cys Phe Lys Arg Gln Glu 50 55 60 Lys Leu His Arg Cys Gly Gln Cys Lys Phe Ala His Tyr Cys Asp 65 70 75 Arg Thr Cys Gln Lys Asp Ala Trp Leu Asn His Lys Asn Glu Cys 80 85 90 Ser Ala Ile Lys Arg Tyr Gly Lys Val Pro Asn Glu Asn Ile Arg 95 100 105 Leu Ala Ala Arg Ile Met Trp Arg Val Glu Arg Glu Gly Thr Gly 110 115 120 Leu Thr Glu Gly Cys Leu Val Ser Val Asp Asp Leu Gln Asn His 125 130 135 Val Glu His Phe Gly Glu Glu Glu Gln Lys Asp Leu Arg Val Asp 140 145 150 Val Asp Thr Phe Leu Gln Tyr Trp Pro Pro Gln Ser Gln Gln Phe 155 160 165 Ser Met Gln Tyr Ile Ser His Ile Phe Gly Val Ile Asn Cys Asn 170 175 180 Gly Phe Thr Leu Ser Asp Gln Arg Gly Leu Gln Ala Val Gly Val 185 190 195 Gly Ile Phe Pro Asn Leu Gly Leu Val Asn His Asp Cys Trp Pro 200 205 210 Asn Cys Thr Val Ile Phe Asn Asn Gly Asn His Glu Ala Val Lys 215 220 225 Ser Met Phe His Thr Gln Met Arg Ile Glu Leu Arg Ala Leu Gly 230 235 240 Lys Ile Ser Glu Gly Glu Glu Leu Thr Val Ser Tyr Ile Asp Phe 245 250 255 Leu Asn Val Ser Glu Glu Arg Lys Arg Gln Leu Lys Lys Gln Tyr 260 265 270 Tyr Phe Asp Cys Thr Cys Glu His Cys Gln Lys Lys Leu Lys Asp 275 280 285 Asp Leu Phe Leu Gly Val Lys Asp Asn Pro Lys Pro Ser Gln Glu 290 295 300 Val Val Lys Glu Met Ile Gln Phe Ser Lys Asp Thr Leu Glu Lys 305 310 315 Ile Asp Lys Ala Arg Ser Glu Gly Leu Tyr His Glu Val Val Lys 320 325 330 Leu Cys Arg Glu Cys Leu Glu Lys Gln Glu Pro Val Phe Ala Asp 335 340 345 Thr Asn Ile Tyr Met Leu Arg Met Leu Ser Ile Val Ser Glu Val 350 355 360 Leu Ser Tyr Leu Gln Ala Phe Glu Glu Ala Ser Phe Tyr Ala Arg 365 370 375 Arg Met Val Asp Gly Tyr Met Lys Leu Tyr His Pro Asn Asn Ala 380 385 390 Gln Leu Gly Met Ala Val Met Arg Ala Gly Leu Thr Asn Trp His 395 400 405 Ala Gly Asn Ile Glu Val Gly His Gly Met Ile Cys Lys Ala Tyr 410 415 420 Ala Ile Leu Leu Val Thr His Gly Pro Ser His Pro Ile Thr Lys 425 430 435 Asp Leu Glu Ala Met Arg Val Gln Thr Glu Met Glu Leu Arg Met 440 445 450 Phe Arg Gln Asn Glu Phe Met Tyr Tyr Lys Met Arg Glu Ala Ala 455 460 465 Leu Asn Asn Gln Pro Met Gln Val Met Ala Glu Pro Ser Asn Glu 470 475 480 Pro Ser Pro Ala Leu Phe His Lys Lys Gln 485 490 11 599 PRT Homo sapiens misc_feature Incyte ID No 4900076CD1 11 Met Met Leu Pro Tyr Pro Ser Ala Leu Gly Asp Gln Tyr Trp Glu 1 5 10 15 Glu Ile Leu Leu Pro Lys Asn Gly Glu Asn Val Glu Thr Met Lys 20 25 30 Lys Leu Thr Gln Asn His Lys Ala Lys Gly Leu Pro Ser Asn Asp 35 40 45 Thr Asp Cys Pro Gln Lys Lys Glu Gly Lys Ala Gln Ile Val Val 50 55 60 Pro Val Thr Phe Arg Asp Val Thr Val Ile Phe Thr Glu Ala Glu 65 70 75 Trp Lys Arg Leu Ser Pro Glu Gln Arg Asn Leu Tyr Lys Glu Val 80 85 90 Met Leu Glu Asn Tyr Arg Asn Leu Leu Ser Leu Ala Glu Pro Lys 95 100 105 Pro Glu Ile Tyr Thr Cys Ser Ser Cys Leu Leu Ala Phe Ser Cys 110 115 120 Gln Gln Phe Leu Ser Gln His Val Leu Gln Ile Phe Leu Gly Leu 125 130 135 Cys Ala Glu Asn His Phe His Pro Gly Asn Ser Ser Pro Gly His 140 145 150 Trp Lys Gln Gln Gly Gln Gln Tyr Ser His Val Ser Cys Trp Phe 155 160 165 Glu Asn Ala Glu Gly Gln Glu Arg Gly Gly Gly Ser Lys Pro Trp 170 175 180 Ser Ala Arg Thr Glu Glu Arg Glu Thr Ser Arg Ala Phe Pro Ser 185 190 195 Pro Leu Gln Arg Gln Ser Ala Ser Pro Arg Lys Gly Asn Met Val 200 205 210 Val Glu Thr Glu Pro Ser Ser Ala Gln Arg Pro Asn Pro Val Gln 215 220 225 Leu Asp Lys Gly Leu Lys Glu Leu Glu Thr Leu Arg Phe Gly Ala 230 235 240 Ile Asn Cys Arg Glu Tyr Glu Pro Asp His Asn Leu Glu Ser Asn 245 250 255 Phe Ile Thr Asn Pro Arg Thr Leu Leu Gly Lys Lys Pro Tyr Ile 260 265 270 Cys Ser Asp Cys Gly Arg Ser Phe Lys Asp Arg Ser Thr Leu Ile 275 280 285 Arg His His Arg Ile His Ser Met Glu Lys Pro Tyr Val Cys Ser 290 295 300 Glu Cys Gly Arg Gly Phe Ser Gln Lys Ser Asn Leu Ser Arg His 305 310 315 Gln Arg Thr His Ser Glu Glu Lys Pro Tyr Leu Cys Arg Glu Cys 320 325 330 Gly Gln Ser Phe Arg Ser Lys Ser Ile Leu Asn Arg His Gln Trp 335 340 345 Thr His Ser Glu Glu Lys Pro Tyr Val Cys Ser Glu Cys Gly Arg 350 355 360 Gly Phe Ser Glu Lys Ser Ser Phe Ile Arg His Gln Arg Thr His 365 370 375 Ser Gly Glu Lys Pro Tyr Val Cys Leu Glu Cys Gly Arg Ser Phe 380 385 390 Cys Asp Lys Ser Thr Leu Arg Lys His Gln Arg Ile His Ser Gly 395 400 405 Glu Lys Pro Tyr Val Cys Arg Glu Cys Gly Arg Gly Phe Ser Gln 410 415 420 Asn Ser Asp Leu Ile Lys His Gln Arg Thr His Leu Asp Glu Lys 425 430 435 Pro Tyr Val Cys Arg Glu Cys Gly Arg Gly Phe Cys Asp Lys Ser 440 445 450 Thr Leu Ile Ile His Glu Arg Thr His Ser Gly Glu Lys Pro Tyr 455 460 465 Val Cys Gly Glu Cys Gly Arg Gly Phe Ser Arg Lys Ser Leu Leu 470 475 480 Leu Val His Gln Arg Thr His Ser Gly Glu Lys His Tyr Val Cys 485 490 495 Arg Glu Cys Arg Arg Gly Phe Ser Gln Lys Ser Asn Leu Ile Arg 500 505 510 His Gln Arg Thr His Ser Asn Glu Lys Pro Tyr Ile Cys Arg Glu 515 520 525 Cys Gly Arg Gly Phe Cys Asp Lys Ser Thr Leu Ile Val His Glu 530 535 540 Arg Thr His Ser Gly Glu Lys Pro Tyr Val Cys Ser Glu Cys Gly 545 550 555 Arg Gly Phe Ser Arg Lys Ser Leu Leu Leu Val His Gln Arg Thr 560 565 570 His Ser Gly Glu Lys His Tyr Val Cys Arg Glu Cys Gly Arg Gly 575 580 585 Phe Ser His Lys Ser Asn Leu Ile Arg His Gln Arg Thr His 590 595 12 365 PRT Homo sapiens misc_feature Incyte ID No 1543848CD1 12 Met Ala Ala Ala Ala Ala Gly Thr Ala Thr Ser Gln Arg Phe Phe 1 5 10 15 Gln Ser Phe Ser Asp Ala Leu Ile Asp Glu Asp Pro Gln Ala Ala 20 25 30 Leu Glu Glu Leu Thr Lys Ala Leu Glu Gln Lys Pro Asp Asp Ala 35 40 45 Gln Tyr Tyr Cys Gln Arg Ala Tyr Cys His Ile Leu Leu Gly Asn 50 55 60 Tyr Cys Val Ala Val Ala Asp Ala Lys Lys Ser Leu Glu Leu Asn 65 70 75 Pro Asn Asn Ser Thr Ala Met Leu Arg Lys Gly Ile Cys Glu Tyr 80 85 90 His Glu Lys Asn Tyr Ala Ala Ala Leu Glu Thr Phe Thr Glu Gly 95 100 105 Gln Lys Leu Asp Ile Glu Thr Gly Phe His Arg Val Gly Gln Ala 110 115 120 Gly Leu Gln Leu Leu Thr Ser Ser Asp Pro Pro Ala Leu Asp Ser 125 130 135 Gln Ser Ala Gly Ile Thr Gly Ala Asp Ala Asn Phe Ser Val Trp 140 145 150 Ile Lys Arg Cys Gln Glu Ala Gln Asn Gly Ser Glu Ser Glu Val 155 160 165 Trp Thr His Gln Ser Lys Ile Lys Tyr Asp Trp Tyr Gln Thr Glu 170 175 180 Ser Gln Val Val Ile Thr Leu Met Ile Lys Asn Val Gln Lys Asn 185 190 195 Asp Val Asn Val Glu Phe Ser Glu Lys Glu Leu Ser Ala Leu Val 200 205 210 Lys Leu Pro Ser Gly Glu Asp Tyr Asn Leu Lys Leu Glu Leu Leu 215 220 225 His Pro Ile Ile Pro Glu Gln Ser Thr Phe Lys Val Leu Ser Thr 230 235 240 Lys Ile Glu Ile Lys Leu Lys Lys Pro Glu Ala Val Arg Trp Glu 245 250 255 Lys Leu Glu Gly Gln Gly Asp Val Pro Thr Pro Lys Gln Phe Val 260 265 270 Ala Asp Val Lys Asn Leu Tyr Pro Ser Ser Ser Pro Tyr Thr Arg 275 280 285 Asn Trp Asp Lys Leu Val Gly Glu Ile Lys Glu Glu Glu Lys Asn 290 295 300 Glu Lys Leu Glu Gly Asp Ala Ala Leu Asn Arg Leu Phe Gln Gln 305 310 315 Ile Tyr Ser Asp Gly Ser Asp Glu Val Lys Arg Ala Met Asn Lys 320 325 330 Ser Phe Met Glu Ser Gly Gly Thr Val Leu Ser Thr Asn Trp Ser 335 340 345 Asp Val Gly Lys Arg Lys Val Glu Ile Asn Pro Pro Asp Asp Met 350 355 360 Glu Trp Lys Lys Tyr 365 13 365 PRT Homo sapiens misc_feature Incyte ID No 6254070CD1 13 Met Ala Gly Ser Ala Met Ser Ser Lys Phe Phe Leu Val Ala Leu 1 5 10 15 Ala Ile Phe Phe Ser Phe Ala Gln Val Val Ile Glu Ala Asn Ser 20 25 30 Trp Trp Ser Leu Gly Met Asn Asn Pro Val Gln Met Ser Glu Val 35 40 45 Tyr Ile Ile Gly Ala Gln Pro Leu Cys Ser Gln Leu Ala Gly Leu 50 55 60 Ser Gln Gly Gln Lys Lys Leu Cys His Leu Tyr Gln Asp His Met 65 70 75 Gln Tyr Ile Gly Glu Gly Ala Lys Thr Gly Ile Lys Glu Cys Gln 80 85 90 Tyr Gln Phe Arg His Arg Arg Trp Asn Cys Ser Thr Val Asp Asn 95 100 105 Thr Ser Val Phe Gly Arg Val Met Gln Ile Gly Ser Arg Glu Thr 110 115 120 Ala Phe Thr Tyr Ala Val Ser Ala Ala Gly Val Val Asn Ala Met 125 130 135 Ser Arg Ala Cys Arg Glu Gly Glu Leu Ser Thr Cys Gly Cys Ser 140 145 150 Arg Ala Ala Arg Pro Lys Asp Leu Pro Arg Asp Trp Leu Trp Gly 155 160 165 Gly Cys Gly Asp Asn Ile Asp Tyr Gly Tyr Arg Phe Ala Lys Glu 170 175 180 Phe Val Asp Ala Arg Glu Arg Glu Arg Ile His Ala Lys Gly Ser 185 190 195 Tyr Glu Ser Ala Arg Ile Leu Met Asn Leu His Asn Asn Glu Ala 200 205 210 Gly Arg Arg Thr Val Tyr Asn Leu Ala Asp Val Ala Cys Lys Cys 215 220 225 His Gly Val Ser Gly Ser Cys Ser Leu Lys Thr Cys Trp Leu Gln 230 235 240 Leu Ala Asp Phe Arg Lys Val Gly Asp Ala Leu Lys Glu Lys Tyr 245 250 255 Asp Ser Ala Ala Ala Met Arg Leu Asn Ser Arg Gly Lys Leu Val 260 265 270 Gln Val Asn Ser Arg Phe Asn Ser Pro Thr Thr Gln Asp Leu Val 275 280 285 Tyr Ile Asp Pro Ser Pro Asp Tyr Cys Val Arg Asn Glu Ser Thr 290 295 300 Gly Ser Leu Gly Thr Gln Gly Arg Leu Cys Asn Lys Thr Ser Glu 305 310 315 Gly Met Asp Gly Cys Glu Leu Met Cys Cys Gly Arg Gly Tyr Asp 320 325 330 Gln Phe Lys Thr Val Gln Thr Glu Arg Cys His Cys Lys Phe His 335 340 345 Trp Cys Cys Tyr Val Lys Cys Lys Lys Cys Thr Glu Ile Val Asp 350 355 360 Gln Phe Val Cys Lys 365 14 203 PRT Homo sapiens misc_feature Incyte ID No 1289839CD1 14 Met Val Ser Thr Tyr Arg Val Ala Val Leu Gly Ala Arg Gly Val 1 5 10 15 Gly Lys Ser Ala Ile Val Arg Gln Phe Leu Tyr Asn Glu Phe Ser 20 25 30 Glu Val Cys Val Pro Thr Thr Ala Arg Arg Leu Tyr Leu Pro Ala 35 40 45 Val Val Met Asn Gly His Val His Asp Leu Gln Ile Leu Asp Phe 50 55 60 Pro Pro Ile Ser Ala Phe Pro Val Asn Thr Leu Gln Glu Trp Ala 65 70 75 Asp Thr Cys Cys Arg Gly Leu Arg Ser Val His Ala Tyr Ile Leu 80 85 90 Val Tyr Asp Ile Cys Cys Phe Asp Ser Phe Glu Tyr Val Lys Thr 95 100 105 Ile Arg Gln Gln Ile Leu Glu Thr Arg Val Ile Gly Thr Ser Glu 110 115 120 Thr Pro Ile Ile Ile Val Gly Asn Lys Arg Asp Leu Gln Arg Gly 125 130 135 Arg Val Ile Pro Arg Trp Asn Val Ser His Leu Val Arg Lys Thr 140 145 150 Trp Lys Cys Gly Tyr Val Glu Cys Ser Ala Lys Tyr Asn Trp His 155 160 165 Ile Leu Leu Leu Phe Ser Glu Leu Leu Lys Ser Val Gly Cys Ala 170 175 180 Arg Cys Lys His Val His Ala Ala Leu Arg Phe Gln Gly Ala Leu 185 190 195 Arg Arg Asn Arg Cys Ala Ile Met 200 15 403 PRT Homo sapiens misc_feature Incyte ID No 5565648CD1 15 Met Glu Pro Val Gly Cys Cys Gly Glu Cys Arg Gly Ser Ser Val 1 5 10 15 Asp Pro Arg Ser Thr Phe Val Leu Ser Asn Leu Ala Glu Val Val 20 25 30 Glu Arg Val Leu Thr Phe Leu Pro Ala Lys Ala Leu Leu Arg Val 35 40 45 Ala Cys Val Cys Arg Leu Trp Arg Glu Cys Val Arg Arg Val Leu 50 55 60 Arg Thr His Arg Ser Val Thr Trp Ile Ser Ala Gly Leu Ala Glu 65 70 75 Ala Gly His Leu Glu Gly His Cys Leu Val Arg Val Val Ala Glu 80 85 90 Glu Leu Glu Asn Val Arg Ile Leu Pro His Thr Val Leu Tyr Met 95 100 105 Ala Asp Ser Glu Thr Phe Ile Ser Leu Glu Glu Cys Arg Gly His 110 115 120 Lys Arg Ala Arg Lys Arg Thr Ser Met Glu Thr Ala Leu Ala Leu 125 130 135 Glu Lys Leu Phe Pro Lys Gln Cys Gln Val Leu Gly Ile Val Thr 140 145 150 Pro Gly Ile Val Val Thr Pro Met Gly Ser Gly Ser Asn Arg Pro 155 160 165 Gln Glu Ile Glu Ile Gly Glu Ser Gly Phe Ala Leu Leu Phe Pro 170 175 180 Gln Ile Glu Gly Ile Lys Ile Gln Pro Phe His Phe Ile Lys Asp 185 190 195 Pro Lys Asn Leu Thr Leu Glu Arg His Gln Leu Thr Glu Val Gly 200 205 210 Leu Leu Asp Asn Pro Glu Leu Arg Val Val Leu Val Phe Gly Tyr 215 220 225 Asn Cys Cys Lys Val Gly Ala Ser Asn Tyr Leu Gln Gln Val Val 230 235 240 Ser Thr Phe Ser Asp Met Asn Ile Ile Leu Ala Gly Gly Gln Val 245 250 255 Asp Asn Leu Ser Ser Leu Thr Ser Glu Lys Asn Pro Leu Asp Ile 260 265 270 Asp Ala Ser Gly Val Val Gly Leu Ser Phe Ser Gly His Arg Ile 275 280 285 Gln Ser Ala Thr Val Leu Leu Asn Glu Asp Val Ser Asp Glu Lys 290 295 300 Thr Ala Glu Ala Ala Met Gln Arg Leu Lys Ala Ala Asn Ile Pro 305 310 315 Glu His Asn Thr Ile Gly Phe Met Phe Ala Cys Val Gly Arg Gly 320 325 330 Phe Gln Tyr Tyr Arg Ala Lys Gly Asn Val Glu Ala Asp Ala Phe 335 340 345 Arg Lys Phe Phe Pro Ser Val Pro Leu Phe Gly Phe Phe Gly Asn 350 355 360 Gly Glu Ile Gly Cys Asp Arg Ile Val Thr Gly Asn Phe Ile Leu 365 370 375 Arg Lys Cys Asn Glu Val Lys Asp Asp Asp Leu Phe His Ser Tyr 380 385 390 Thr Thr Ile Met Ala Leu Ile His Leu Gly Ser Ser Lys 395 400 16 1022 PRT Homo sapiens misc_feature Incyte ID No 2764456CD1 16 Met Tyr Phe Cys Trp Gly Ala Asp Ser Arg Glu Leu Gln Arg Arg 1 5 10 15 Arg Thr Ala Gly Ser Pro Gly Ala Glu Leu Leu Gln Ala Ala Ser 20 25 30 Gly Glu Arg His Ser Leu Leu Leu Leu Thr Asn His Arg Val Leu 35 40 45 Ser Cys Gly Asp Asn Ser Arg Gly Gln Leu Gly Arg Arg Gly Ala 50 55 60 Gln Arg Gly Glu Leu Pro Glu Pro Ile Gln Ala Leu Glu Thr Leu 65 70 75 Ile Val Asp Leu Val Ser Cys Gly Lys Glu His Ser Leu Ala Val 80 85 90 Cys His Lys Gly Arg Val Phe Ala Trp Gly Ala Gly Ser Glu Gly 95 100 105 Gln Leu Gly Ile Gly Glu Phe Lys Glu Ile Ser Phe Thr Pro Lys 110 115 120 Lys Ile Met Thr Leu Asn Asp Ile Lys Ile Ile Gln Val Ser Cys 125 130 135 Gly His Tyr His Ser Leu Ala Leu Ser Lys Asp Ser Gln Val Phe 140 145 150 Ser Trp Gly Lys Asn Ser His Gly Gln Leu Gly Leu Gly Lys Glu 155 160 165 Phe Pro Ser Gln Ala Ser Pro Gln Arg Val Arg Ser Leu Glu Gly 170 175 180 Ile Pro Leu Ala Gln Val Ala Ala Gly Gly Ala His Ser Phe Ala 185 190 195 Leu Ser Leu Cys Gly Thr Ser Phe Gly Trp Gly Ser Asn Ser Ala 200 205 210 Gly Gln Leu Ala Leu Ser Gly Arg Asn Val Pro Val Gln Ser Asn 215 220 225 Lys Pro Leu Ser Val Gly Ala Leu Lys Asn Leu Gly Val Val Tyr 230 235 240 Ile Ser Cys Gly Asp Ala His Thr Ala Val Leu Thr Gln Asp Gly 245 250 255 Lys Val Phe Thr Phe Gly Asp Asn Arg Ser Gly Gln Leu Gly Tyr 260 265 270 Ser Pro Thr Pro Glu Lys Arg Gly Pro Gln Leu Val Glu Arg Ile 275 280 285 Asp Gly Leu Val Ser Gln Ile Asp Cys Gly Ser Tyr His Thr Leu 290 295 300 Ala Tyr Val His Thr Thr Gly Gln Val Val Ser Phe Gly His Gly 305 310 315 Pro Ser Asp Thr Ser Lys Pro Thr His Pro Glu Ala Leu Thr Glu 320 325 330 Asn Phe Asp Ile Ser Cys Leu Ile Ser Ala Glu Asp Phe Val Asp 335 340 345 Val Gln Val Lys His Ile Phe Ala Gly Thr Tyr Ala Asn Phe Val 350 355 360 Thr Thr His Gln Asp Thr Ser Ser Thr Arg Ala Pro Gly Lys Thr 365 370 375 Leu Pro Glu Ile Ser Arg Ile Ser Gln Ser Met Ala Glu Lys Trp 380 385 390 Ile Ala Val Lys Arg Arg Ser Thr Glu His Glu Met Ala Lys Ser 395 400 405 Glu Ile Arg Met Ile Phe Ser Ser Pro Ala Cys Leu Thr Ala Ser 410 415 420 Phe Leu Lys Lys Arg Gly Thr Gly Glu Thr Thr Ser Ile Asp Val 425 430 435 Asp Leu Glu Met Ala Arg Asp Thr Phe Lys Lys Leu Thr Lys Lys 440 445 450 Glu Trp Ile Ser Ser Met Ile Thr Thr Cys Leu Glu Asp Asp Leu 455 460 465 Leu Arg Ala Leu Pro Cys His Ser Pro His Gln Glu Ala Leu Ser 470 475 480 Val Phe Leu Leu Leu Pro Glu Cys Pro Val Met His Asp Ser Lys 485 490 495 Asn Trp Lys Asn Leu Val Val Pro Phe Ala Lys Ala Val Cys Glu 500 505 510 Met Ser Lys Gln Ser Leu Gln Val Leu Lys Lys Cys Trp Ala Phe 515 520 525 Leu Gln Glu Ser Ser Leu Asn Pro Leu Ile Gln Met Leu Lys Ala 530 535 540 Ala Ile Ile Ser Gln Leu Leu His Gln Thr Lys Thr Glu Gln Asp 545 550 555 His Cys Asn Val Lys Ala Leu Leu Gly Met Met Lys Glu Leu His 560 565 570 Lys Val Asn Lys Ala Asn Cys Arg Leu Pro Glu Asn Thr Phe Asn 575 580 585 Ile Asn Glu Leu Ser Asn Leu Leu Asn Phe Tyr Ile Asp Arg Gly 590 595 600 Arg Gln Leu Phe Arg Asp Asn His Leu Ile Pro Ala Glu Thr Pro 605 610 615 Ser Pro Val Ile Phe Ser Asp Phe Pro Phe Ile Phe Asn Ser Leu 620 625 630 Ser Lys Ile Lys Leu Leu Gln Ala Asp Ser His Ile Lys Met Gln 635 640 645 Met Ser Glu Lys Lys Ala Tyr Met Leu Met His Glu Thr Ile Leu 650 655 660 Gln Lys Lys Asp Glu Phe Pro Pro Ser Pro Arg Phe Ile Leu Arg 665 670 675 Val Arg Arg Ser Arg Leu Val Lys Asp Ala Leu Arg Gln Leu Ser 680 685 690 Gln Ala Glu Ala Thr Asp Phe Cys Lys Val Leu Val Val Glu Phe 695 700 705 Ile Asn Glu Ile Cys Pro Glu Ser Gly Gly Val Ser Ser Glu Phe 710 715 720 Phe His Cys Met Phe Glu Glu Met Thr Lys Pro Glu Tyr Gly Met 725 730 735 Phe Met Tyr Pro Glu Met Gly Ser Cys Met Trp Phe Pro Ala Lys 740 745 750 Pro Lys Pro Glu Lys Lys Arg Tyr Phe Leu Phe Gly Met Leu Cys 755 760 765 Gly Leu Ser Leu Phe Asn Leu Asn Val Ala Asn Leu Pro Phe Pro 770 775 780 Leu Ala Leu Tyr Lys Lys Leu Leu Asp Gln Lys Pro Ser Leu Glu 785 790 795 Asp Leu Lys Glu Leu Ser Pro Arg Leu Gly Lys Ser Leu Gln Glu 800 805 810 Val Leu Asp Asp Ala Ala Asp Asp Ile Gly Asp Ala Leu Cys Ile 815 820 825 Arg Phe Ser Ile His Trp Asp Gln Asn Asp Val Asp Leu Ile Pro 830 835 840 Asn Gly Ile Ser Ile Pro Val Asp Gln Thr Asn Lys Arg Asp Tyr 845 850 855 Val Ser Lys Tyr Ile Asp Tyr Ile Phe Asn Val Ser Val Lys Ala 860 865 870 Val Tyr Glu Glu Phe Gln Arg Gly Phe Tyr Arg Val Cys Glu Lys 875 880 885 Glu Ile Leu Arg His Phe Tyr Pro Glu Glu Leu Met Thr Ala Ile 890 895 900 Ile Gly Asn Thr Asp Tyr Asp Trp Lys Gln Phe Glu Gln Asn Ser 905 910 915 Lys Tyr Glu Gln Gly Tyr Gln Lys Ser His Pro Thr Ile Gln Leu 920 925 930 Phe Trp Lys Ala Phe His Lys Leu Thr Leu Asp Glu Lys Lys Lys 935 940 945 Phe Leu Phe Phe Leu Thr Gly Arg Asp Arg Leu His Ala Arg Gly 950 955 960 Ile Gln Lys Met Glu Ile Val Phe Arg Cys Pro Glu Thr Phe Ser 965 970 975 Glu Arg Asp His Pro Thr Ser Ile Thr Cys His Asn Ile Leu Ser 980 985 990 Leu Pro Lys Tyr Ser Thr Met Glu Arg Met Glu Glu Ala Leu Gln 995 1000 1005 Val Ala Ile Asn Asn Asn Arg Gly Phe Val Ser Pro Met Leu Thr 1010 1015 1020 Gln Ser 17 1462 PRT Homo sapiens misc_feature Incyte ID No 5734806CD1 17 Met Gly Ala Gln Asp Arg Pro Gln Cys His Phe Asp Ile Glu Ile 1 5 10 15 Asn Arg Glu Pro Val Gly Arg Ile Met Phe Gln Leu Phe Ser Asp 20 25 30 Ile Cys Pro Lys Thr Cys Lys Asn Phe Leu Cys Leu Cys Ser Gly 35 40 45 Glu Lys Gly Leu Gly Lys Thr Thr Gly Lys Lys Leu Cys Tyr Lys 50 55 60 Gly Ser Thr Phe His Arg Val Val Lys Asn Phe Met Ile Gln Gly 65 70 75 Gly Asp Phe Ser Glu Gly Asn Gly Lys Gly Gly Glu Ser Ile Tyr 80 85 90 Gly Gly Tyr Phe Lys Asp Glu Asn Phe Ile Leu Lys His Asp Arg 95 100 105 Ala Phe Leu Leu Ser Met Ala Asn Arg Gly Lys His Thr Asn Gly 110 115 120 Ser Gln Phe Phe Ile Thr Thr Lys Pro Ala Pro His Leu Asp Gly 125 130 135 Val His Val Val Phe Gly Leu Val Ile Ser Gly Phe Glu Val Ile 140 145 150 Glu Gln Ile Glu Asn Leu Lys Thr Asp Ala Ala Ser Arg Pro Tyr 155 160 165 Ala Asp Val Arg Val Ile Asp Cys Gly Val Leu Ala Thr Lys Ser 170 175 180 Ile Lys Asp Val Phe Glu Lys Lys Arg Lys Lys Pro Thr His Ser 185 190 195 Glu Gly Ser Asp Ser Ser Ser Asn Ser Ser Ser Ser Ser Glu Ser 200 205 210 Ser Ser Glu Ser Glu Leu Glu His Glu Arg Ser Arg Arg Arg Lys 215 220 225 His Lys Arg Arg Pro Lys Val Lys Arg Ser Lys Lys Arg Arg Lys 230 235 240 Glu Ala Ser Ser Ser Glu Glu Pro Arg Asn Lys His Ala Met Asn 245 250 255 Pro Lys Gly His Ser Glu Arg Ser Asp Thr Asn Glu Lys Arg Ser 260 265 270 Val Asp Ser Ser Ala Lys Arg Glu Lys Pro Val Val Arg Pro Glu 275 280 285 Glu Ile Pro Pro Val Pro Glu Asn Arg Phe Leu Leu Arg Arg Asp 290 295 300 Met Pro Val Val Thr Ala Glu Pro Glu Pro Ile Pro Asp Val Ala 305 310 315 Pro Ile Val Ser Asp Gln Lys Pro Ser Val Ser Lys Ser Gly Arg 320 325 330 Lys Ile Lys Gly Arg Gly Thr Ile Arg Tyr His Thr Pro Pro Arg 335 340 345 Ser Arg Ser Cys Ser Glu Ser Asp Asp Asp Asp Ser Ser Glu Thr 350 355 360 Pro Pro His Trp Lys Glu Glu Met Gln Arg Leu Arg Ala Tyr Arg 365 370 375 Pro Pro Ser Gly Glu Lys Trp Ser Lys Gly Asp Lys Leu Ser Asp 380 385 390 Pro Cys Ser Ser Arg Trp Asp Glu Arg Ser Leu Ser Gln Arg Ser 395 400 405 Arg Ser Trp Ser Tyr Asn Gly Tyr Tyr Ser Asp Leu Ser Thr Ala 410 415 420 Arg His Ser Gly His His Lys Lys Arg Arg Lys Glu Lys Lys Val 425 430 435 Lys His Lys Lys Lys Gly Lys Lys Gln Lys His Cys Arg Arg His 440 445 450 Lys Gln Thr Lys Lys Arg Arg Ile Leu Ile Pro Ser Asp Ile Glu 455 460 465 Ser Ser Lys Ser Ser Thr Arg Arg Met Lys Ser Ser Cys Asp Arg 470 475 480 Glu Arg Ser Ser Arg Ser Ser Ser Leu Ser Ser His His Ser Ser 485 490 495 Lys Arg Asp Trp Ser Lys Ser Asp Lys Asp Val Gln Ser Ser Leu 500 505 510 Thr His Ser Ser Arg Asp Ser Tyr Arg Ser Lys Ser His Ser Gln 515 520 525 Ser Tyr Ser Arg Gly Ser Ser Arg Ser Arg Thr Ala Ser Lys Ser 530 535 540 Ser Ser His Ser Arg Ser Arg Ser Lys Ser Arg Ser Ser Ser Lys 545 550 555 Ser Gly His Arg Lys Arg Ala Ser Lys Ser Pro Arg Lys Thr Ala 560 565 570 Ser Gln Leu Ser Glu Asn Lys Pro Val Lys Thr Glu Pro Leu Arg 575 580 585 Ala Thr Met Ala Gln Asn Glu Asn Val Val Val Gln Pro Val Val 590 595 600 Ala Glu Asn Ile Pro Val Ile Pro Leu Ser Asp Ser Pro Pro Pro 605 610 615 Ser Arg Trp Lys Pro Gly Gln Lys Pro Trp Lys Pro Ser Tyr Glu 620 625 630 Arg Ile Gln Glu Met Lys Ala Lys Thr Thr His Leu Leu Pro Ile 635 640 645 Gln Ser Thr Tyr Ser Leu Ala Asn Ile Lys Glu Thr Gly Ser Ser 650 655 660 Ser Ser Tyr His Lys Arg Glu Lys Asn Ser Glu Ser Asp Gln Ser 665 670 675 Thr Tyr Ser Lys Tyr Ser Asp Arg Ser Ser Glu Ser Ser Pro Arg 680 685 690 Ser Arg Ser Arg Ser Ser Arg Ser Arg Ser Tyr Ser Arg Ser Tyr 695 700 705 Thr Arg Ser Arg Ser Leu Ala Ser Ser His Ser Arg Ser Arg Ser 710 715 720 Pro Ser Ser Arg Ser His Ser Arg Asn Lys Tyr Ser Asp His Ser 725 730 735 Gln Cys Ser Arg Ser Ser Ser Tyr Thr Ser Ile Ser Ser Asp Asp 740 745 750 Gly Arg Arg Ala Lys Arg Arg Leu Arg Ser Ser Gly Lys Lys Asn 755 760 765 Ser Val Ser His Lys Lys His Ser Ser Ser Ser Glu Lys Thr Leu 770 775 780 His Ser Lys Tyr Val Lys Gly Arg Asp Arg Ser Ser Cys Val Arg 785 790 795 Lys Tyr Ser Glu Ser Arg Ser Ser Leu Asp Tyr Ser Ser Asp Ser 800 805 810 Glu Gln Ser Ser Val Gln Ala Thr Gln Ser Ala Gln Glu Lys Glu 815 820 825 Lys Gln Gly Gln Met Glu Arg Thr His Asn Lys Gln Glu Lys Asn 830 835 840 Arg Gly Glu Glu Lys Ser Lys Ser Glu Arg Glu Cys Pro His Ser 845 850 855 Lys Lys Arg Thr Leu Lys Glu Asn Leu Ser Asp His Leu Arg Asn 860 865 870 Gly Ser Lys Pro Lys Arg Lys Asn Tyr Ala Gly Ser Lys Trp Asp 875 880 885 Ser Glu Ser Asn Ser Glu Arg Asp Val Thr Lys Asn Ser Lys Asn 890 895 900 Asp Ser His Pro Ser Ser Asp Lys Glu Glu Gly Glu Ala Thr Ser 905 910 915 Asp Ser Glu Ser Glu Val Ser Glu Ile His Ile Lys Val Lys Pro 920 925 930 Thr Thr Lys Ser Ser Thr Asn Thr Ser Leu Pro Asp Asp Asn Gly 935 940 945 Ala Trp Lys Ser Ser Lys Gln Arg Thr Ser Thr Ser Asp Ser Glu 950 955 960 Gly Ser Cys Ser Asn Ser Glu Asn Asn Arg Gly Lys Pro Gln Lys 965 970 975 His Lys His Gly Ser Lys Glu Asn Leu Lys Arg Glu His Thr Lys 980 985 990 Lys Val Lys Glu Lys Leu Lys Gly Lys Lys Asp Lys Lys His Lys 995 1000 1005 Ala Pro Lys Arg Lys Gln Ala Phe His Trp Gln Pro Pro Leu Glu 1010 1015 1020 Phe Gly Glu Glu Glu Glu Glu Glu Ile Asp Asp Lys Gln Val Thr 1025 1030 1035 Gln Glu Ser Lys Glu Lys Lys Val Ser Glu Asn Asn Glu Thr Ile 1040 1045 1050 Lys Asp Asn Ile Leu Lys Thr Glu Lys Ser Ser Glu Glu Asp Leu 1055 1060 1065 Ser Gly Lys His Asp Thr Val Thr Val Ser Ser Asp Leu Asp Gln 1070 1075 1080 Phe Thr Lys Asp Asp Ser Lys Leu Ser Ile Ser Pro Thr Ala Leu 1085 1090 1095 Asn Thr Glu Glu Asn Val Ala Cys Leu Gln Asn Ile Gln His Val 1100 1105 1110 Glu Glu Ser Val Pro Asn Gly Val Glu Asp Val Leu Gln Thr Asp 1115 1120 1125 Asp Asn Met Glu Ile Cys Thr Pro Asp Arg Ser Ser Pro Ala Lys 1130 1135 1140 Val Glu Glu Thr Ser Pro Leu Gly Asn Ala Arg Leu Asp Thr Pro 1145 1150 1155 Asp Ile Asn Ile Val Leu Lys Gln Asp Met Ala Thr Glu His Pro 1160 1165 1170 Gln Ala Glu Val Val Lys Gln Glu Ser Ser Met Ser Glu Ser Lys 1175 1180 1185 Val Leu Gly Glu Val Gly Lys Gln Asp Ser Ser Ser Ala Ser Leu 1190 1195 1200 Ala Ser Ala Gly Glu Ser Thr Gly Lys Lys Glu Val Ala Glu Lys 1205 1210 1215 Ser Gln Ile Asn Leu Ile Asp Lys Lys Trp Lys Pro Leu Gln Gly 1220 1225 1230 Val Gly Asn Leu Ala Ala Pro Asn Ala Ala Thr Ser Ser Ala Val 1235 1240 1245 Glu Val Lys Val Leu Thr Thr Val Pro Glu Met Lys Pro Gln Gly 1250 1255 1260 Leu Arg Ile Glu Ile Lys Ser Lys Asn Lys Val Arg Pro Gly Ser 1265 1270 1275 Leu Phe Asp Glu Val Arg Lys Thr Ala Arg Leu Asn Arg Arg Pro 1280 1285 1290 Arg Asn Gln Glu Ser Ser Ser Asp Glu Gln Thr Pro Ser Arg Asp 1295 1300 1305 Asp Asp Ser Gln Ser Arg Ser Pro Ser Arg Ser Arg Ser Lys Ser 1310 1315 1320 Glu Thr Lys Ser Arg His Arg Thr Arg Ser Val Ser Tyr Ser His 1325 1330 1335 Ser Arg Ser Arg Ser Arg Ser Ser Thr Ser Ser Tyr Arg Ser Arg 1340 1345 1350 Ser Tyr Ser Arg Ser Arg Ser Arg Gly Trp Tyr Ser Arg Gly Arg 1355 1360 1365 Thr Arg Ser Arg Ser Ser Ser Tyr Arg Ser Tyr Lys Ser His Arg 1370 1375 1380 Thr Ser Ser Arg Ser Arg Ser Arg Ser Ser Ser Tyr Asp Pro His 1385 1390 1395 Ser Arg Ser Ser Arg Ser Tyr Thr Tyr Asp Ser Tyr Tyr Ser Arg 1400 1405 1410 Ser Arg Ser Arg Ser Arg Ser Gln Arg Ser Asp Ser Tyr His Arg 1415 1420 1425 Gly Arg Ser Tyr Asn Arg Arg Ser Arg Ser Cys Arg Ser Tyr Gly 1430 1435 1440 Ser Asp Ser Glu Ser Asp Arg Ser Tyr Ser His His Arg Ser Pro 1445 1450 1455 Ser Glu Ser Ser Arg Tyr Ser 1460 18 329 PRT Homo sapiens misc_feature Incyte ID No 7495168CD1 18 Met Ser Ala Glu Ala Ser Gly Pro Ala Ala Ala Ala Ala Pro Ser 1 5 10 15 Leu Glu Ala Pro Lys Pro Ser Gly Leu Glu Pro Gly Pro Ala Ala 20 25 30 Tyr Gly Leu Lys Pro Leu Thr Pro Asn Ser Lys Tyr Val Lys Leu 35 40 45 Asn Val Gly Gly Ser Leu His Tyr Thr Thr Leu Arg Thr Leu Thr 50 55 60 Gly Gln Asp Thr Met Leu Lys Ala Met Phe Ser Gly Arg Val Glu 65 70 75 Val Leu Thr Asp Ala Gly Gly Trp Val Leu Ile Asp Arg Ser Gly 80 85 90 Arg His Phe Gly Thr Ile Leu Asn Tyr Leu Arg Asp Gly Ser Val 95 100 105 Pro Leu Pro Glu Ser Thr Arg Glu Leu Gly Glu Leu Leu Gly Glu 110 115 120 Ala Arg Tyr Tyr Leu Val Gln Gly Leu Ile Glu Asp Cys Gln Leu 125 130 135 Ala Leu Gln Gln Lys Arg Glu Thr Leu Ser Pro Leu Cys Leu Ile 140 145 150 Pro Met Val Thr Ser Pro Arg Glu Glu Gln Gln Leu Leu Ala Ser 155 160 165 Thr Ser Lys Pro Val Val Lys Leu Leu His Asn Arg Ser Asn Asn 170 175 180 Lys Tyr Ser Tyr Thr Ser Thr Ser Asp Asp Asn Leu Leu Lys Asn 185 190 195 Ile Glu Leu Phe Asp Lys Leu Ala Leu Arg Phe His Gly Arg Leu 200 205 210 Leu Phe Leu Lys Asp Val Leu Gly Asp Glu Ile Cys Cys Trp Ser 215 220 225 Phe Tyr Gly Gln Gly Arg Lys Ile Ala Glu Val Cys Cys Thr Ser 230 235 240 Ile Val Tyr Ala Thr Glu Lys Lys Gln Thr Lys Val Glu Phe Pro 245 250 255 Glu Ala Arg Ile Phe Glu Glu Thr Leu Asn Ile Leu Ile Tyr Glu 260 265 270 Thr Pro Arg Gly Pro Asp Pro Ala Leu Leu Glu Ala Thr Gly Gly 275 280 285 Ala Ala Gly Ala Gly Gly Ala Gly Arg Gly Glu Asp Glu Glu Asn 290 295 300 Arg Glu His Arg Val Arg Arg Ile His Val Arg Arg His Ile Thr 305 310 315 His Asp Glu Arg Pro His Gly Gln Gln Ile Val Phe Lys Asp 320 325 19 476 PRT Homo sapiens misc_feature Incyte ID No 7483131CD1 19 Met Val Lys Leu Ile His Thr Leu Ala Asp His Gly Asp Asp Val 1 5 10 15 Asn Cys Cys Ala Phe Ser Phe Ser Leu Leu Ala Thr Cys Ser Leu 20 25 30 Asp Lys Thr Ile Arg Leu Tyr Ser Leu Arg Asp Phe Thr Glu Leu 35 40 45 Pro His Ser Pro Leu Lys Phe His Thr Tyr Ala Val His Cys Cys 50 55 60 Cys Phe Ser Pro Ser Gly His Ile Leu Ala Ser Cys Ser Thr Asp 65 70 75 Gly Thr Thr Val Leu Trp Asn Thr Glu Asn Gly Gln Met Leu Ala 80 85 90 Val Met Glu Gln Pro Ser Gly Ser Pro Val Arg Val Cys Gln Phe 95 100 105 Ser Pro Asp Ser Thr Cys Leu Ala Ser Gly Ala Ala Asp Gly Thr 110 115 120 Val Val Leu Trp Asn Ala Gln Ser Tyr Lys Leu Tyr Arg Cys Gly 125 130 135 Ser Val Lys Asp Gly Ser Leu Ala Ala Cys Ala Phe Ser Pro Asn 140 145 150 Gly Ser Phe Phe Val Thr Gly Ser Ser Cys Gly Asp Leu Thr Val 155 160 165 Trp Asp Asp Lys Met Arg Cys Leu His Ser Glu Lys Ala His Asp 170 175 180 Leu Gly Ile Thr Cys Cys Asp Phe Ser Ser Gln Pro Val Ser Asp 185 190 195 Gly Glu Gln Gly Leu Gln Phe Phe Arg Leu Ala Ser Cys Gly Gln 200 205 210 Asp Cys Gln Val Lys Ile Trp Ile Val Ser Phe Thr His Ile Leu 215 220 225 Gly Phe Glu Leu Lys Tyr Lys Ser Thr Leu Ser Gly His Cys Ala 230 235 240 Pro Val Leu Ala Cys Ala Phe Ser His Asp Gly Gln Met Leu Val 245 250 255 Ser Gly Ser Val Asp Lys Ser Val Ile Val Tyr Asp Thr Asn Thr 260 265 270 Glu Asn Ile Leu His Thr Leu Thr Gln His Thr Arg Tyr Val Thr 275 280 285 Thr Cys Ala Phe Ala Pro Asn Thr Leu Leu Leu Ala Thr Gly Ser 290 295 300 Met Asp Lys Thr Val Asn Ile Trp Gln Phe Asp Leu Glu Thr Leu 305 310 315 Cys Gln Ala Arg Ser Thr Glu His Gln Leu Lys Gln Phe Thr Glu 320 325 330 Asp Trp Ser Glu Glu Asp Val Ser Thr Trp Leu Cys Ala Gln Asp 335 340 345 Leu Lys Asp Leu Val Gly Ile Phe Lys Met Asn Asn Ile Asp Gly 350 355 360 Lys Glu Leu Leu Asn Leu Thr Lys Glu Ser Leu Ala Asp Asp Leu 365 370 375 Lys Ile Glu Ser Leu Gly Leu Arg Ser Lys Val Leu Arg Lys Ile 380 385 390 Glu Glu Leu Arg Thr Lys Val Lys Ser Leu Ser Ser Gly Ile Pro 395 400 405 Asp Glu Phe Ile Cys Pro Ile Thr Arg Glu Leu Met Lys Asp Pro 410 415 420 Val Ile Ala Ser Asp Gly Tyr Ser Tyr Glu Lys Glu Ala Met Glu 425 430 435 Asn Trp Ile Ser Lys Lys Lys Arg Thr Ser Pro Met Thr Asn Leu 440 445 450 Val Leu Pro Ser Ala Val Leu Thr Pro Asn Arg Thr Leu Lys Met 455 460 465 Ala Ile Asn Arg Trp Leu Glu Thr His Gln Lys 470 475 20 485 PRT Homo sapiens misc_feature Incyte ID No 4558650CD1 20 Met Ala Leu Pro Pro Phe Phe Gly Gln Gly Arg Pro Gly Pro Pro 1 5 10 15 Pro Pro Gln Pro Pro Pro Pro Ala Pro Phe Gly Cys Pro Pro Pro 20 25 30 Pro Leu Pro Ser Pro Ala Phe Pro Pro Pro Leu Pro Gln Arg Pro 35 40 45 Gly Pro Phe Pro Gly Ala Ser Ala Pro Phe Leu Gln Pro Pro Leu 50 55 60 Ala Leu Gln Pro Arg Ala Ser Ala Glu Ala Ser Arg Gly Gly Gly 65 70 75 Gly Ala Gly Ala Phe Tyr Pro Val Pro Pro Pro Pro Leu Pro Pro 80 85 90 Pro Pro Pro Gln Cys Arg Pro Phe Pro Gly Thr Asp Ala Gly Glu 95 100 105 Arg Pro Arg Pro Pro Pro Pro Gly Pro Gly Pro Pro Trp Ser Pro 110 115 120 Arg Trp Pro Glu Ala Pro Pro Pro Pro Ala Asp Val Leu Gly Asp 125 130 135 Ala Ala Leu Gln Arg Leu Arg Asp Arg Gln Trp Leu Glu Ala Val 140 145 150 Phe Gly Thr Pro Arg Arg Ala Gly Cys Pro Val Pro Gln Arg Thr 155 160 165 His Ala Gly Pro Ser Leu Gly Glu Val Arg Ala Arg Leu Leu Arg 170 175 180 Ala Leu Arg Leu Val Arg Arg Leu Arg Gly Leu Ser Gln Ala Leu 185 190 195 Arg Glu Ala Glu Ala Asp Gly Ala Ala Trp Val Leu Leu Tyr Ser 200 205 210 Gln Thr Ala Pro Leu Arg Ala Glu Leu Ala Glu Arg Leu Gln Pro 215 220 225 Leu Thr Gln Ala Ala Tyr Val Gly Glu Ala Arg Arg Arg Leu Glu 230 235 240 Arg Val Arg Arg Arg Arg Leu Arg Leu Arg Glu Arg Ala Arg Glu 245 250 255 Arg Glu Ala Glu Arg Glu Ala Glu Ala Ala Arg Ala Val Glu Arg 260 265 270 Glu Gln Glu Ile Asp Arg Trp Arg Val Lys Cys Val Gln Glu Val 275 280 285 Glu Glu Lys Lys Arg Glu Gln Glu Leu Lys Ala Ala Ala Asp Gly 290 295 300 Val Leu Ser Glu Val Arg Lys Lys Gln Ala Asp Thr Lys Arg Met 305 310 315 Val Asp Ile Leu Arg Ala Leu Glu Lys Leu Arg Lys Leu Arg Lys 320 325 330 Glu Ala Ala Ala Arg Lys Gly Val Cys Pro Pro Ala Ser Ala Asp 335 340 345 Glu Thr Phe Thr His His Leu Gln Arg Leu Arg Lys Leu Ile Lys 350 355 360 Lys Arg Ser Glu Leu Tyr Glu Ala Glu Glu Arg Ala Leu Arg Val 365 370 375 Met Leu Glu Gly Glu Gln Glu Glu Glu Arg Lys Arg Glu Leu Glu 380 385 390 Lys Lys Gln Arg Lys Glu Glu Glu Lys Ile Leu Leu Gln Lys Arg 395 400 405 Glu Ile Glu Ser Lys Leu Phe Gly Asp Pro Asp Glu Phe Pro Leu 410 415 420 Ala His Leu Leu Glu Pro Phe Arg Gln Tyr Tyr Leu Gln Ala Glu 425 430 435 His Ser Leu Pro Ala Leu Ile Gln Ile Arg His Asp Trp Asp Gln 440 445 450 Tyr Leu Val Pro Ser Asp His Pro Lys Gly Asn Phe Val Pro Gln 455 460 465 Gly Trp Val Leu Pro Pro Leu Pro Ser Asn Asp Ile Trp Ala Thr 470 475 480 Ala Val Lys Leu His 485 21 406 PRT Homo sapiens misc_feature Incyte ID No 7506195CD1 21 Met Ala Leu Pro Pro Phe Phe Gly Gln Gly Arg Pro Gly Pro Pro 1 5 10 15 Pro Pro Gln Pro Pro Pro Pro Ala Pro Phe Gly Cys Pro Pro Pro 20 25 30 Pro Leu Pro Ser Pro Ala Phe Pro Pro Pro Leu Pro Gln Arg Pro 35 40 45 Gly Pro Phe Pro Gly Ala Ser Ala Pro Phe Leu Gln Pro Pro Leu 50 55 60 Ala Leu Gln Pro Arg Ala Ser Ala Glu Ala Ser Arg Gly Gly Gly 65 70 75 Gly Ala Gly Ala Phe Tyr Pro Val Pro Pro Pro Pro Leu Pro Pro 80 85 90 Pro Pro Pro Gln Cys Arg Pro Phe Pro Gly Thr Asp Ala Gly Glu 95 100 105 Arg Pro Arg Pro Pro Pro Pro Gly Pro Gly Pro Pro Trp Ser Pro 110 115 120 Arg Trp Pro Glu Ala Pro Pro Pro Pro Ala Asp Val Leu Gly Asp 125 130 135 Ala Ala Leu Gln Arg Leu Arg Asp Arg Gln Trp Leu Glu Ala Val 140 145 150 Phe Gly Thr Pro Arg Arg Ala Gly Cys Pro Val Pro Gln Arg Thr 155 160 165 His Ala Gly Pro Ser Leu Gly Glu Val Arg Ala Arg Leu Leu Arg 170 175 180 Ala Leu Arg Leu Val Arg Arg Leu Arg Gly Leu Ser Gln Ala Leu 185 190 195 Arg Glu Ala Glu Ala Asp Gly Ala Ala Trp Val Leu Leu Tyr Ser 200 205 210 Gln Thr Ala Pro Leu Arg Ala Glu Leu Ala Glu Arg Leu Gln Pro 215 220 225 Leu Thr Gln Ala Ala Tyr Val Gly Glu Ala Arg Arg Arg Leu Glu 230 235 240 Arg Val Arg Arg Arg Arg Leu Arg Leu Arg Glu Arg Ala Arg Glu 245 250 255 Arg Glu Ala Glu Arg Glu Ala Glu Ala Ala Arg Ala Val Glu Arg 260 265 270 Glu Gln Glu Ile Asp Arg Trp Arg Val Lys Cys Val Gln Glu Val 275 280 285 Glu Glu Lys Lys Arg Glu Gln Glu Leu Lys Ala Ala Ala Asp Gly 290 295 300 Val Leu Ser Glu Val Arg Lys Lys Gln Ala Asp Thr Lys Arg Met 305 310 315 Val Asp Ile Leu Arg Ala Leu Glu Lys Leu Arg Lys Leu Arg Lys 320 325 330 Glu Ala Ala Ala Arg Lys Asp Glu Phe Pro Leu Ala His Leu Leu 335 340 345 Glu Pro Phe Arg Gln Tyr Tyr Leu Gln Ala Glu His Ser Leu Pro 350 355 360 Ala Leu Ile Gln Ile Arg His Asp Trp Asp Gln Tyr Leu Val Pro 365 370 375 Ser Asp His Pro Lys Gly Asn Phe Val Pro Gln Gly Trp Val Leu 380 385 390 Pro Pro Leu Pro Ser Asn Asp Ile Trp Ala Thr Ala Val Lys Leu 395 400 405 His 22 7742 DNA Homo sapiens misc_feature Incyte ID No 1351608CB1 22 ggtactgaga ggatggaaat cagcgcggag ttaccccaga cccctcagcg tctggcatct 60 tggtgggatc agcaagttga tttttatact gctttcttgc atcatttggc acaattggtg 120 ccagaaattt actttgctga aatggaccca gacttggaaa agcaggagga aagtgtacaa 180 atgtcaatat tcactccact ggaatggtac ttatttggag aagatccaga tatttgctta 240 gagaaattga agcacagtgg agcatttcag ctttgtggga gggttttcaa aagtggagag 300 acaacctatt cttgcaggga ttgtgcaatt gatccaacat gtgtactctg tatggactgc 360 ttccaggaca gtgttcataa aaatcatcgt tacaagatgc atacttctac tggaggaggg 420 ttctgtgact gtggagacac agaggcatgg aaaactggcc ctttttgtgt aaatcatgaa 480 cctggaagag caggtactat aaaagagaat tcacgctgtc cgttgaatga agaggtaatt 540 gtccaagcca ggaaaatatt tccttcagtg ataaaatatg tcgtagaaat gactatatgg 600 gaagaggaaa aagaactgcc tcctgaactc cagataaggg agaaaaatga aagatactat 660 tgtgtccttt tcaatgatga acaccattca tatgaccacg tcatatacag cctacaaaga 720 gctcttgact gtgagctcgc agaggcccag ttgcatacca ctgccattga caaagagggt 780 cgtcgggctg ttaaagcggg agcttatgct gcttgccagg aagcaaagga agatataaag 840 agtcattcag aaaatgtctc tcaacatcca cttcatgtag aagtattaca ctcagagatt 900 atggctcatc agaaatttgc tttgcgtctt ggttcctgga tgaacaaaat tatgagctat 960 tcaagtgact ttaggcagat cttttgccaa gcatgcctta gagaagaacc tgactcggag 1020 aatccctgtc tcataagcag gttaatgctt tgggatgcaa agctttataa aggtgcccgt 1080 aagatccttc atgaattgat cttcagcagt ttttttatgg agatggaata caaaaaactc 1140 tttgctatgg aatttgtgaa gtattataaa caactgcaga aagaatatat cagtgatgat 1200 catgacagaa gtatctctat aactgcactt tcagttcaga tgtttactgt tcctactctg 1260 gctcgacatc ttattgaaga gcagaatgtt atctctgtca ttactgaaac tctgctagaa 1320 gttttacctg agtacttgga caggaacaat aaattcaact tccagggtta tagccaggac 1380 aaattgggaa gagtatatgc agtaatatgt gacctaaagt atatcctgat cagcaaaccc 1440 acaatatgga cagaaagatt aagaatgcag ttccttgaag gttttcgatc ttttttgaag 1500 attcttacct gtatgcaggg aatggaagaa atccgaagac aggttgggca acacattgaa 1560 gtggatcctg attgggaggc tgccattgct atacagatgc aattgaagaa tattttactc 1620 atgttccaag agtggtgtgc ttgtgatgaa gaactcttac ttgtggctta taaagaatgt 1680 cacaaagctg tgatgaggtg cagtaccagt ttcatatcta gtagcaagac agtagtacaa 1740 tcgtgtggac atagtttgga aacaaagtcc tacagagtat ctgaggatct tgtaagcata 1800 catctgccac tctctaggac ccttgctggt cttcatgtac gtttaagcag gctgggtgct 1860 gtttcaagac tgcatgaatt tgtgtctttt gaggactttc aagtagaggt actagtggaa 1920 tatcctttac gttgtctggt gttggttgcc caggttgttg ctgagatgtg gcgaagaaat 1980 ggactgtctc ttattagcca ggtgttttat taccaagatg ttaagtgcag agaagaaatg 2040 tatgataaag atatcatcat gcttcagatt ggtgcatctt taatggatcc caataagttc 2100 ttgttactgg tacttcagag gtatgaactt gccgaggctt ttaacaagac catatctaca 2160 aaagaccagg atttgattaa acaatataat acactaatag aagaaatgct tcaggtcctc 2220 atctatattg tgggtgagcg ttatgtacct ggagtgggaa atgtgaccaa agaagaggtc 2280 acaatgagag aaatcattca cttgctttgc attgaaccca tgccacacag tgccattgcc 2340 aaaaatttac ctgagaatga aaataatgaa actggcttag agaatgtcat aaacaaagtg 2400 gccacattta agaaaccagg tgtatcaggc catggagttt atgaactaaa agatgaatca 2460 ctgaaagact tcaatatgta cttttatcat tactccaaaa cccagcatag caaggctgaa 2520 catatgcaga agaaaaggag aaaacaagaa aacaaagatg aagcattgcc gccaccacca 2580 cctcctgaat tctgccctgc tttcagcaaa gtgattaacc ttctcaactg tgatatcatg 2640 atgtacattc tcaggaccgt atttgagcgg gcaatagaca cagattctaa cttgtggacc 2700 gaagggatgc tccaaatggc ttttcatatt ctggcattgg gtttactaga agagaagcaa 2760 cagcttcaaa aagctcctga agaagaagta acatttgact tttatcataa ggcttcaaga 2820 ttgggaagtt cagccatgaa tatacaaatg cttttggaaa aactcaaagg aattccccag 2880 ttagaaggcc agaaggacat gataacgtgg atacttcaga tgtttgacac agtgaagcga 2940 ttaagagaaa aatcttgttt aattgtagca accacatcag gatcggaatc tattaagaat 3000 gatgagatta ctcatgataa agaaaaagca gaacgaaaaa gaaaagctga agctgctagg 3060 ctacatcgcc agaagatcat ggctcagatg tctgccttac agaaaaactt cattgaaact 3120 cataaactca tgtatgacaa tacatcagaa atgcctggga aagaagattc cattatggag 3180 gaagagagca ccccagcagt cagtgactac tctagaattg ctttgggtcc taaacggggt 3240 ccatctgtta ctgaaaagga ggtgctgacg tgcatccttt gccaagaaga acaggaggtg 3300 aaaatagaaa ataatgccat ggtattatcg gcctgtgtcc agaaatctac tgccttaacc 3360 cagcacaggg gaaaacccat agaactctca ggagaagccc tagacccact tttcatggat 3420 ccagacttgg catatggaac ttatacagga agctgtggtc atgtaatgca cgcagtgtgc 3480 tggcagaagt attttgaagc tgtacagctg agctctcagc agcgcattca tgttgacctt 3540 tttgacttgg aaagtggaga atatctttgc cctctttgca aatctctgtg caatactgtg 3600 atccccatta ttcctttgca acctcaaaag ataaacagtg agaatgcaga tgctcttgct 3660 caacttttga ccctggcacg gtggatacag actgttctgg ccagaatatc aggttataat 3720 ataagacatg ctaaaggaga aaacccaatt cctattttct ttaatcaagg aatgggagat 3780 tctactttgg agttccattc catcctgagt tttggcgttg agtcttcgat taaatattca 3840 aatagcatca aggaaatggt tattctcttt gccacaacaa tttatagaat tggattgaaa 3900 gtgccacctg atgaaaggga tcctcgagtc cccatgctga cctggagcac ctgcgctttc 3960 actatccagg caattgaaaa tctattggga gatgaaggaa aacctctgtt tggagcactt 4020 caaaataggc agcataatgg tctgaaagca ttaatgcagt ttgcagttgc acagaggatt 4080 acctgtcctc aggtcctgat acagaaacat ctggttcgtc ttctatcagt tgttcttcct 4140 aacataaaat cagaagatac accatgcctt ctgtctatag atctgtttca tgttttggtg 4200 ggtgctgtgt tagcattccc atccttgtat tgggatgacc ctgttgatct gcagccttct 4260 tcagttagtt cttcctataa ccacctttat ctcttccatt tgatcaccat ggcacacatg 4320 cttcagatac tacttacagt agacacaggc ctaccccttg ctcaggttca agaagacagt 4380 gaagaggctc attccgcatc ttctttcttt gcagaaattt ctcaatatac aagtggctcc 4440 attgggtgtg atattcctgg ctggtatttg tgggtctcac tgaagaatgg catcacccct 4500 tatcttcgct gtgctgcatt gtttttccac tatttacttg gggtaactcc gcctgaggaa 4560 ctgcatacca attctgcaga aggagagtac agtgcactct gtagctatct atctttacct 4620 acaaatttgt tcctgctctt ccaggaatat tgggatactg taaggccctt gctccagagg 4680 tggtgtgcag atcctgcctt actaaactgt ttgaagcaaa aaaacaccgt ggtcaggtac 4740 cctagaaaaa gaaatagttt gatagagctt cctgatgact atagctgcct cctgaatcaa 4800 gcttctcatt tcaggtgccc acggtctgca gatgatgagc gaaagcatcc tgtcctctgc 4860 cttttctgtg gggctatact atgttctcag aacatttgct gccaggaaat tgtgaacggg 4920 gaagaggttg gagcttgcat ttttcacgca cttcactgtg gagccggagt ctgcattttc 4980 ctaaaaatca gagaatgccg agtggtcctg gttgaaggta aagccagagg ctgtgcctat 5040 ccagctcctt acttggatga atatggagaa acagaccctg gcctgaagag gggcaacccc 5100 cttcatttat ctcgtgagcg gtatcggaag ctccatttgg tctggcaaca acactgcatt 5160 atagaagaga ttgctaggag ccaagagact aatcagatgt tatttggatt caactggcag 5220 ttactgtgag ctccaactct gcctcaagac aatcacaaat gacgacagta gtaaaggctg 5280 attcaaaatt atggaaaact ttctgagggc tgggaaagta ttggagggtc ttttgctcca 5340 tgtccaggtt cacttacatc aataaaatat ttcttaatgg agtattgctt tcaattagca 5400 aacatatgct tcacaggaaa aaaggacata gatcaatctg ttttatgtgc tagtatttcc 5460 aggaatttat tccccttcat aatttgtctc atttcatttt atttcatcca cttggtagat 5520 gaagtcacgt caaacagttg tagacatttt atgtgttggt taactcttct gcaattttgt 5580 atttggtgtt ttccccccaa gtttagttca actgacattg gatcactgac aaaattctaa 5640 taatctgtga tagtcttcct tgcagttaaa gaagaattgc agaaaccatg caatatactt 5700 gggaaagatt ccaaaaataa attttttatt atttctcttt taaggaaata cccctaatgt 5760 gccacctgct gctatcacca caaattaaac tcaatctcta tgtggacaga ggatgatttc 5820 tgccaatatg gaaaagcttt tttctcactg taggcctcaa gaaaagttag ggtaatgtat 5880 ttgttattca ttcctgacgg tacaaagagc ttgcagttct cacctctgac taccagtagc 5940 tttgttgagt tttgaaataa tacttgacat tttccaaagg caaatctcat tctgcaagga 6000 gattgtggca ccatcctgtt tgactctcag aaacctcttg taattctgat gtaaaaactg 6060 tagaatgaag atgagaaaat tctcgcaatg agtggatcat gacaactgta aattagaaca 6120 atcagattta aaccaattcc gcaatcttct atatctttgt aaaagacaaa tccttgatgt 6180 tgtctgtgtg caaccttttc ataaactctg gttttatgac tagtacaaac caccaaaaaa 6240 gccatgtgat caatagtctg tgtcctgtta taacatgctg tggttgagcc atcttgttta 6300 taaataatag agctctcctg aatttgtgca tagacttctt ggttcctggc ttttgttttt 6360 tgtatcaaga gattgtgata taaaacagca gaagataaat ggaaaccttc cattttaact 6420 tacgttgttt ctggggtaat gttagaacct tgaaagatgc attcaaagac tgtatcttat 6480 tttgcccttg gctattagtg tctcacatat gtgtgtaaat gttttcctac cttctttttg 6540 ctcagcaaag gcaagcaagt aaaatatatt tgctaagtga ttagtgatgc acatttgggg 6600 ctagattttt ttggtacttt tatgtaaaga aaagtggatt ttgcagtaag ggattggcat 6660 gagcaggcgt cagaatcaca atcatgattt tctacttgaa taattacaat tcagaaggta 6720 tctggataaa tagatacatg tctagtgaac aatttgtaac aataacaggt aaggatcagg 6780 aaattcagta ttcagtttgt cagatttgcc agaatgatga aagtatttga acatgtgtgt 6840 ttgtttctta tataattgta ttgagtggat tgtttgactg ggaaatctgg gctagaatag 6900 gaaacagaag atactgactt ctaccctaat agatgggccc caatttagca aagataaact 6960 gactttattt ttagtccttt ttatattaac ttaataaatt ctggagttag gctctcaaga 7020 ggacagaggg actgtctggc aatggccagc cagaccttta ctgccaaaga acccatttca 7080 tattgcgttc cactgattga gattgattca gatttttgca ctgtagatga gcgtatgtct 7140 cagtgctgcc ccaagcccca gggatttctc attatgttca aatgtcctag tgatttacct 7200 taatcattgc aaacaattat gcttatgaag tttacttaca aacaagcaac tgagtcactt 7260 tattttcttt agtgtagtat gtgaaggcac tggttcaaca ggatggctcc agaactgtgt 7320 ttttctaatg tttggtaagg ggctagtgag aattttaatg atatggtgaa gaaaaatata 7380 tctgtataat taatttatta tattggtgta tgggctgtga gttcaccttt tagtggtcat 7440 ttgtcatttc ataacaacta tgcattttgg ttcactgtga tgatgatcta tatttagtga 7500 ctgcaacatg tttataccac tgattcaaat tccatccatg atgaagttat acaaataatg 7560 catatattga taacttttat tgcaaaaatg taaatttaaa acttgtataa tgttcttgtg 7620 ctttttaaaa taaaatatat gtgtatattt aaaaagaaaa aaaaaaaaaa aaaaaaaaaa 7680 aaaaaaaaaa aaaaaaaaaa aaaaaaaaaa aaaaaaaaaa aacgaaaaaa aaaggggcgc 7740 cc 7742 23 1674 DNA Homo sapiens misc_feature Incyte ID No 4259314CB1 23 ggcggcggtg tctcaggcgg caatggaagg atccgagcct gtggccgccc atcaggggga 60 agaggcgtcc tgttcttcct gggggactgg cagcacaaat aaaaatttgc ccattatgtc 120 aacagcatct gtggaaatcg atgatgcatt gtatagtcga cagaggtacg ttcttggaga 180 cacagcaatg cagaagatgg ccaagtccca tgttttctta agtgggatgg gtggtcttgg 240 tttggaaatt gcaaagaatc ttgttcttgc agggattaag gcagttacaa ttcatgatac 300 agaaaaatgc caagcatggg atctaggaac caacttcttt ctcagtgaag atgatgttgt 360 taataagaga aacagggctg aagctgtact taaacatatt gcagaactaa atccatacgt 420 tcatgtcaca tcatcttctg ttcctttcaa tgagaccaca gatctctcct ttttagataa 480 ataccagtgt gtagtattga ctgagatgaa acttccattg cagaagaaga tcaatgactt 540 ttgccgttct cagtgccctc caattaagtt tatcagtgca gatgtacatg gaatttggtc 600 aaggttattt tgtgatttcg gtgatgaatt tgaagtttta gatacaacag gagaagaacc 660 aaaagaaatt ttcatttcaa acataacgca agcaaatcct ggcattgtta cttgccttga 720 aaatcatcct cacaaactgg agacaggaca attcctaaca tttcgagaaa ttaatggaat 780 gacaggttta aatggatcta tacaacaaat aacggtgata tcgccatttt cttttagtat 840 tggtgacacc acagaactgg aaccatattt acatggaggc atagctgtcc aagttaagac 900 tcctaaaaca gttttttttg aatcactgga gaggcagtta aaacatccaa agtgccttat 960 tgtggatttt agcaaccctg aggcaccttt agagattcac acagctatgc ttgccttgga 1020 ccagtttcag gagaaataca gtcgcaagcc aaatgttgga tgccaacaag attcagaaga 1080 actgttgaaa ctagcaacat ctataagtga aaccttggaa gagaaggtga ctattgaaat 1140 ttatggctgt ccgaatattt gtttgttaat acataagtgt tctgtatatt agtattctct 1200 tatccttcac atccagcttt gctactctgt ggcattagac aacttttttc agtttgttct 1260 gttttaattt ataaatctat aaaatagagt taacctacct tcatagggtt attgtgaaca 1320 ttaaataatt taattttgta aagtacttag aaatgccatg tgacatatag taattaatat 1380 ttgctgctat ttttttaact gttactatta ttctttatta ttctgttatg atttacttga 1440 tttgttaacc cacttaaact tatatatgtt agctttctta tataagtcac ctgttttata 1500 tattatacat tcatatctct ttatcacatt tcgtacatca gatttagatt taaacatttc 1560 acctagaaaa tggttttttt gtgtgtgtta tgatgccagt gcctgcttgt caacagtttt 1620 atttgagcag ctataaacat ggtgatgttt gtgcaattaa aaaaaaaaaa aggg 1674 24 3671 DNA Homo sapiens misc_feature Incyte ID No 3660046CB1 24 agcagaggtg tgtacgggca ctgctttaaa actgggaagg aggaagacga ggccaggagc 60 tggagggtca ccaaggtaga tttccagcag cgctagtcca gctgaacact ttccagcctt 120 gtttttcagc agctttgagg aaaagtatag tgatccgtat gtgaaacttt cattgtacgt 180 agcggatgag aatagagaac ttgctttggt ccagacaaaa acaattaaaa agacactgaa 240 cccaaaatgg aatgaagaat tttatttcag ggtaaaccca tctaatcaca gactcctatt 300 tgaagtattt gacgaaaata gactgacacg agacgacttc ctgggccagg tggacgtgcc 360 ccttagtcac cttccgacag aagatccaac catggagcga ccctatacat ttaaggactt 420 tctcctcaga ccaagaagtc ataagtctcg agttaaggga tttttgcgat tgaaaatggc 480 ctatatgcca aaaaatggag gtcaagatga agaaaacagt gaccagaggg atgacatgga 540 gcatggatgg gaagttgttg actcaaatga ctcggcttct cagcaccaag aggaacttcc 600 tcctcctcct ctgcctcccg ggtgggaaga aaaagtggac aatttaggcc gaacttacta 660 tgtcaaccac aacaaccgga ccactcagtg gcacagacca agcctgatgg acgtgtcctc 720 ggagtcggac aataacatca gacagatcaa ccaggaggca gcacaccggc gcttccgctc 780 ccgcaggcac atcagcgaag acttggagcc cgagccctcg gagggcgggg atgtccccga 840 gccttgggag accatttcag aggaagtgaa tatcgctgga gactctctcg gtctggctct 900 gcccccacca ccggcctccc caggatctcg gaccagccct caggagctgt cagaggaact 960 aagcagaagg cttcagatca ctccagactc caatggggaa cagttcagct ctttgattca 1020 aagagaaccc tcctcaaggt tgaggtcatg cagtgtcacc gacgcagttg cagaacaggg 1080 ccatctacca ccgcccagtg ccccagctgg gagagcgcgt tcatcaactg tcacgggtgg 1140 tgaggaacca acgccatcag tggcctatgt acataccacg ccgggtctgc cttcaggctg 1200 ggaagaaaga aaagatgcta aggggcgcac atactatgtc aatcataaca atcgaaccac 1260 aacttggact cgacctatca tgcagcttgc agaagatggt gcgtccggat cagccacaaa 1320 cagtaacaac catctaatcg agcctcagat ccgccggcct cgtagcctca gctcgccaac 1380 agtaacttta tctgccccgc tggagggtgc caaggactca cccgtacgtc gggctgtgaa 1440 agacaccctt tccaacccac agtccccaca gccatcacct tacaactccc ccaaaccaca 1500 acacaaagtc acacagagct tcttgccacc cggctgggaa atgaggatag cgccaaacgg 1560 ccggcccttc ttcattgatc ataacacaaa gactacaacc tgggaagatc cacgtttgaa 1620 atttccagta catatgcggt caaagacatc tttaaacccc aatgatctag ggcctttacc 1680 tccaggatgg gaagagagaa ctcacacaga tggaagaatc ttctacataa atcacaatat 1740 aaaaagaaca caatgggaag atcctcggtt ggagaatgta gcaataactg gaccagcagt 1800 gccctactcc agggattaca aaagaaagta tgagttcttc cgaagaaagt tgaagaagca 1860 gaatgacatt ccaaacaaat ttgaaatgaa acttcgccga gcaactgttc ttgaagactc 1920 ttaccggaga attatgggtg tcaagagagc agacttcctg aaggctcgac tgtggattga 1980 gtttgatggt gaaaagggat tggattatgg aggagttgcc agagaatggt tcttcctgat 2040 ctcaaaggaa atgtttaacc cttattatgg gttgtttgaa tattctgcta cggacaatta 2100 taccctacag ataaatccaa actctggatt gtgtaacgaa gatcacctct cttacttcaa 2160 gtttattggt cgggtagctg gaatggcagt ttatcatggc aaactgttgg atggtttttt 2220 catccgccca ttttacaaga tgatgcttca caaaccaata acccttcatg atatggaatc 2280 tgtggatagt gaatattaca attccctaag atggattctt gaaaatgacc caacagaatt 2340 ggacctcagg tttatcatag atgaagaact ttttggacag acacatcaac atgagctgaa 2400 aaatggtgga tcagaaatag ttgtcaccaa taagaacaaa aaggaatata tttatcttgt 2460 aatacaatgg cgatttgtaa accgaatcca gaagcaaatg gctgctttta aagagggatt 2520 ctttgaacta ataccacagg atctcatcaa aatttttgat gaaaatgaac tagagcttct 2580 tatgtgtgga ctgggagatg ttgatgtgaa tgactggagg gaacatacaa agtataaaaa 2640 tggctacagt gcaaatcatc aggttataca gtggttttgg aaggctgttt taatgatgga 2700 ttcagaaaaa agaataagat tacttcagtt tgtcactggc acatctcggg tgcctatgaa 2760 tggatttgct gaactatacg gttcaaatgg accacagtca tttacagttg aacagtgggg 2820 tactcctgaa aagctgccaa gagctcatac ctgttttaat cgcctggact tgccacctta 2880 tgaatcattt gaagaattat gggataaact tcagatggca attgaaaaca cccagggctt 2940 tgatggagtt gattagatta caaataacaa tctgtagtgt ttttactgcc atagttttat 3000 aaccaaaatc ttgacttaaa attttccggg gaactactaa aatgtggcca ctgagtcttc 3060 ccagatcttg aagaaaatca tataaaaagc atttgaagaa atagtacgac aacttatttt 3120 taatcacttt taaataatgt gttgcattta cacagttgtt tcattctgtc tttagagtta 3180 ggtgcctgcc taaagccagg caccaccaca cctggcttta gagttcacac aataggatat 3240 aagtcctgta tgacttaaat agtgaatttt gtccttaaca tttacctctt gtatagtatc 3300 tgccaggcag ttttttctta aactactgag atgataactg tgaaatattt gtgatacgtg 3360 tcatgtgtga aaagtttgat gcattttgag atggaaaact gaaatttgga aaaagaaata 3420 ctttactatt gagtaaacta caatatattt agtgctactc gcagctattt attattttgt 3480 agacctgcct tatgcacctt actgcctaga tttttgggaa aaaactttgg aaagtgtgtt 3540 acctatattt ctagccaact aactcacaga aaaactgttt acttcttcac tttcgaagta 3600 tttggctttt gttaatatgc agttttacta aacagatggt tcataagaca tgtgaagcaa 3660 attcatattt g 3671 25 2038 DNA Homo sapiens misc_feature Incyte ID No 3016416CB1 25 cgtttatttc cccaggaaat tttgaataaa gcccaaaggc cagaggggaa cccctttgag 60 gcccaaggga ggtccaaaat ttgaaactga gccaatcgcg ggggacaccc tgaagttcca 120 caaaaaaaat ttacaaggca aattaattgg ggattcatgg cacgaccctg tggttcccgc 180 tacttgggag gctgaggtgg gaggatcacc tgagcccagg aggttgagtc ttgcagtgag 240 gctgagttca caccactgta ctcgagcctt gatgacagaa tgagactgtc tcaaaaaaaa 300 aaaaatgtcc ttaagtccat gtggacccct gactaggttt gtgccctaga cagccgtcct 360 ctgagggcaa ttcaggtggt gagactccag gtttaaatgg cctccacaga aatttcacta 420 acctgccttt gggtttgacc ctgtataacc cctttcttct ggaggtccct ttgggtggca 480 gtagatacgg gatttggtgt ctgacagctc tggggacaga tcccagctcc aaatggcaga 540 gtctctacag attacaagcc aaatacttag cactatgtgc tgatcttcag gaagtcagtc 600 tatatttcat aacaagtcac atggggataa tgaaggaatg gcctaaaatg ctctcagtaa 660 tattcctgag tcatccctca gggctaggct tggtgttagg catggcgggg aagggagcag 720 agctgtgtgc agaggaagat gcagttcttg ccttgtcagg gtccctgacc tgatggcgac 780 ccatggtgga gtcttcatag tgacagacac cactgtaaaa gcagatccag gttgtgcaac 840 cctcaaagca ggtctcctca ctcaccggga tagatagact attggccgta cctgcatcca 900 ccgcttgcca tggtttcgtt gtgggtggag gatactttcc tgtcccctgg ctttgggttt 960 gcccacgtgg cttgctctgg ccttggaatg aagcagaaac gaaaggctgc cagttccgag 1020 cccacgtctg aagtcgcctt aggtggttcc gcgggccccg tgcgctccca ccttcaccca 1080 gagggccttc tctggtgcag ccgctgcttc ttcagcctcc gcccaaaagg aacggagccc 1140 cctggccgat ccgcaggcct acagggagcc acagagcgca gcggctggac cagcgttcaa 1200 gcccaagcac aggcctgcga gaaccttgtt ccagccgccg tttaggatgg ttgattagga 1260 cgcgttgcag tggcggtagc tcaccaatcc agtgcgtgca cccgctcctt tattaggcta 1320 tagagccagt ggctcccaca gggacctgat acaacagtgc gttaaataag gagcatattg 1380 agctctcatg tcgtaagcca gtggagaagt ccagggctag tgtgggggct ccggcggggg 1440 ctgtggcccc catccgcatg gagcctcccc atggttcaca ggtctcagtc ttcggagcct 1500 tcggccctgc gagcccgaac agtccacagg gcggcgccag accctctttc gaacgccatc 1560 ctctaaagcc tcggctccaa ccggttccac ttcttcaggc tcaggatttt cactcttctc 1620 gaatgggggt ggccctcccc caatcttctg agtcgcaaca gcatctccct ccctccagga 1680 cctcagagcc agagctgggc gagaggccct gacctccggg gtagggtgga agcgtccctg 1740 tgaaggtgca gtcctgcctc ccatccccag gcgccgggcc tctcccaccc tcagcgccct 1800 gctcacctcc agctgaagat gccagggcac ctctgcttcc tccctgccct ctctgcagta 1860 ccgccgagtg tgcataaaag ggtttaatat aggctttgcc gggcgcgggg actcccacct 1920 gtaatcccag tacgttgaga gaccaaggcg ggaggatcac ttgaggccag gagttcaaaa 1980 ccagcctggg caacaaagtg aggcccgtct ctgaaaaaaa aaaaaaaaaa aaaagggt 2038 26 2235 DNA Homo sapiens misc_feature Incyte ID No 2133755CB1 26 tccagtgagc ggcggagccc ggagcggcgg gctgggcgcc gggcgggcgg ggctcgcggc 60 tgagaggcgg gcgggccggg ggcgccgggc gcggggccgc catgtggagc ggccgcagct 120 ccttcaccag cttggtggtg ggcgtgttcg tggtctacgt ggtgcacacc tgctgggtca 180 tgtacggcat cgtctacacc cgcccgtgct ccggcgacgc caactgcatc cagccctacc 240 tggcgcggcg gcccaagctg cagctgagcg tgtacaccac gacgaggtcc cacctgggtg 300 ctgagaacaa catcgacctg gtcttgaatg tggaagactt tgatgtggag tccaaatttg 360 aaaggacagt taatgtttct gtaccaaaga aaacgagaaa caatgggacg ctgtatgcct 420 acatcttcct ccatcacgct ggggtcctgc cgtggcacga cgggaagcag gtgcacctgg 480 tcagtcctct gaccacctac atggtcccca agccagaaga aatcaacctg ctcaccgggg 540 agtctgatac acagcagatc gaggcggaga agaagccgac gagtgccctg gatgagccag 600 tgtcccactg gcgaccgcgg ctggcgctga acgtgatggc ggacaacttt gtctttgacg 660 ggtcctccct gcctgccgat gtgcatcggt acatgaagat gatccagctg gggaaaaccg 720 tgcattacct gcccatcctg ttcatcgacc agctcagcaa ccgcgtgaag gacctgatgg 780 tcataaaccg ctccaccacc gagctgcccc tcaccgtgtc ctacgacaag gtctcactgg 840 ggcggctgcg cttctggatc cacatgcagg acgccgtgta ctccctgcag cagttcgggt 900 tttcagagaa agatgctgat gaggtgaaag gaatttttgt agataccaac ttatacttcc 960 tggcgctgac cttctttgtc gcagcgttcc atcttctctt tgatttcctg gcctttaaaa 1020 atgacatcag tttctggaag aagaagaaga gcatgatcgg catgtccacc aaggcagtgc 1080 tctggcgctg cttcagcacc gtggtcatct ttctgttcct gctggacgag cagacgagcc 1140 tgctggtgct ggtcccggcg ggtgttggag ccgccattga gctgtggaaa gtgaagaagg 1200 cattgaagat gactattttt tggagaggcc tgatgcccga atttcagttt ggcacttaca 1260 gcgaatctga gaggaaaacc gaggagtacg atactcaggc catgaagtac ttgtcatacc 1320 tgctgtaccc tctctgtgtc gggggtgctg tctattcact cctgaatatc aaatataaga 1380 gctggtactc ctggttaatc aacagcttcg tcaacggggt ctatgccttt ggtttcctct 1440 tcatgctgcc ccagctcttt gtgaactaca agttgaagtc agtggcacat ctgccctgga 1500 aggccttcac ctacaaggct ttcaacacct tcattgatga cgtctttgcc ttcatcatca 1560 ccatgcccac gtctcaccgg ctggcctgct tccgggacga cgtggtgttt ctggtctacc 1620 tgtaccagcg gtggctttat cctgtggata aacgcagagt gaacgagttt ggggagtcct 1680 acgaggagaa ggccacgcgg gcgccccaca cggactgaag gccgcccggg ctgccgccag 1740 ccaagtgcaa cttgaattgt caatgagtat ttttggaagc atttggagga attcctagac 1800 attgcgtttt ctgtgttgcc aaaatccctt cggacatttc tcagacatct cccaagttcc 1860 catcacgtca gatttggagc tggtagcgct tacgatgccc ccacgtgtga acatctgtct 1920 tggtcacaga gctgggtgct gccggtcacc ttgagctgtg gtggctcccg gcacacgagt 1980 gtccggggtt cggccatgtc ctcacgcggg caggggtggg agccctcaca ggcaaggggg 2040 ctgttggatt tccatttcag gtggttttct aagtgctcct tatgtgaatt tcaaacacgt 2100 atggaattca ttccgcatgg actctgggat caaaggctct ttcctctttt gtttgagagt 2160 tggttgtttt aaagcttaat gtatgtttct attttaaaat aaatttttct ggctgtggca 2220 aaaaaaaaaa aaaaa 2235 27 1851 DNA Homo sapiens misc_feature Incyte ID No 5259957CB1 27 cctggaacta ctgcttgatt ctctgagaga tcccagcacc ctacaaactg agtccagatc 60 tgagttttcc cttgcagatt catcaagatg agcatcaggg ccccacccag actcctggag 120 ctggcaaggc agaggctgct gagggaccag gccttggcca tctccaccat ggaggagctg 180 cccagggagc tcttccccac gctgttcatg gaggccttca gcaggagacg ctgtgaaacc 240 ctgaaaacaa tggtgcaggc ctggcctttc acccgcctcc ctctagggtc cctgatgaag 300 tcgcctcatc tggagtcatt aaaatctgtg ctggaagggg ttgatgtgct gttgacccaa 360 gaggttcgcc ccaggcagtc aaaacttcaa gtgctggact tgaggaatgt ggatgagaac 420 ttctgcgaca tattttctgg agctactgca tccttcccgg aggctctgag tcagaagcaa 480 acagcagata actgtccagg gacaggcagg cagcagccat tcatggtgtt catagacctt 540 tgtctcaaga acaggacact agatgaatgc ctcacccacc tcttagagtg gggcaagcag 600 agaaaaggct tactgcatgt gtgttgcaag gagctgcagg tttttggaat gcccatccac 660 agtatcatag aggtcctgaa catggtggag cttgactgta tccaggaggt ggaagtgtgc 720 tgcccctggg agctgtccac tcttgtgaag tttgcccctt acctgggcca gatgaggaat 780 ctccgcaaac ttgttctctt caacatccgt gcatctgcct gcattccccc agacaacaag 840 gggcagttca ttgcccgatt cacctctcag ttcctcaagc tggactattt ccagaatctg 900 tctatgcact ccgtctcttt cctcgaaggc cacctggacc agctgctcag gtgtctccag 960 gcctccttgg agatggtcgt tatgaccgac tgcctgctgt cagagtcaga cttgaagcat 1020 ctctcttggt gcccgagcat ccgtcaatta aaggagctgg acctgagggg tgtcacgctg 1080 acccatttca gccctgagcc cctcacaggt ctgctggagc aagctgtggc caccctgcag 1140 accctggact tagaggactg tgggatcatg gattcccaac tcagcgccat cctgcctgtc 1200 ctgagccgct gctcccagct cagcaccttc agcttctgtg ggaacctcat ctccatggct 1260 gcccttgaga acctgctgcg ccacaccgtc gggctgagca agctaagcct ggagctgtat 1320 cctgcccctc tggagagtta tgacacccag ggtgctctct gctgggggag atttgctgaa 1380 cttggggctg agctgatgaa cacactgagg gacttaaggc agcccaagat cattgtgttc 1440 tgcaccgtcc cctgccctcg ctgtggcatc agggcctcct atgacctgga gcccagtcac 1500 tgcctctgtt gaatgcctgc catcagggtg gatatatttc aagctttctt ctggtcattt 1560 cggagctgaa acctaggcca tgagtgcatg ttaaagggag cacagaccca tcgtttcaaa 1620 tgcctcctca gtgtgaatgg gaaaggaatg aggatgcagg aggggcagga ctgggggaaa 1680 agttgacttg gagtggatgg gctctttaga gacctgtgtc ccagagaatc agaaatggga 1740 atctgaattg ctagagtgag aatcagggag gagagacaca tgagagggtt acccctgcac 1800 agatggttgt aaagtaacag tcagaaataa agggaaactg agtggaaaga a 1851 28 1466 DNA Homo sapiens misc_feature Incyte ID No 55029783CB1 28 aaagacgcaa gcgtcgcgcg cccaaggctc agcgcgcctg cgcaggatag cggccgttca 60 gccagcggct cgggggcgga agcactggag ccccgagtca cgtggctgcg ggcggagatg 120 agcggggcgt gggacgtgct gcggcgtcct agctggctta cagggcggcg gcggggtgtg 180 tgtcctctgt taagagtgct actcgcccgg ggttgatctg tgcatgccac tcctgggtca 240 gacggtgagg tcggcgtctg cgaggacgcg gcggtggagt agaagggcag ccggagacag 300 gcccggcgcc ccttccgagg ctagacggcc ccagcttcgc ggggatcatg gcattctggt 360 ggaccgagtg cggggccact ggcgaatcgc cgccgggtcc tgttcaacct gctggtgtcc 420 atctgcattg tgttcctcaa caaatggatt tatgtgtacc acgggcttcc ccaacatgag 480 cctgaccctg gtgcacttcg tggtcacctg gctgggcttg tatatctgcc agaagctgga 540 catctttgcc cccaaaagtc tgccgccctc caggctcctc ctcctggccc tcagcttctg 600 tggctttgtg gtcttcacta acctttctct gcagaacaac accataggca cctatcagct 660 ggccaaggcc atgaccacgc cggtgatcat agccatccag accttctgct accagaaaac 720 cttctccacc agaatccagc tcacgctgat tcctataact ttaggtgtaa tcctaaattc 780 ttattacgat gtgaagttta atttccttgg aatggtgttt gctgctcttg gtgttttagt 840 tacatccctt tatcaagtgt gggtaggagc caaacagcat gaattacaag tgaactcaat 900 gcagctgctg tactaccagg ctccgatgtc atctgccatg ttgctggttg ctgtgccctt 960 ctttgagcca gtgtttggag aaggaggaat atttggtccc tggtcagttt ctgctttgct 1020 tatggtgctg ctatctggag taatagcttt catggtgaac ttatcaattt attggatcat 1080 tgggaacact tcacctgtca cctataacat gttcggacac ttcaagttct gcattacttt 1140 attcggagga tatgttttat ttaaggatcc actgtccatt aatcaggccc ttggcatttt 1200 atgtacatta tttggcattc tcgcctatac ccactttaag ctcagtgaac aggaaggaag 1260 taggagtaaa ctggcacaac gtccttaatt gggtttttgt ggagaaaaga atgttgtccc 1320 aagaagataa aaaatattgt taagtgtgca agttattaaa aaaaaaaaat tgggccaggc 1380 acggtggctc acgcctgtaa tcccagcact ttgggaggcc aaggccagcg gatcacttga 1440 ggtcagggag tcgagacagc ctgaca 1466 29 1049 DNA Homo sapiens misc_feature Incyte ID No 8032202CB1 29 gtgcagcccc tccccacagc atgctggggg ctaattctga tgtcatcttt ctgcagaaaa 60 ccattagacc atccctccag actgccaccc tcaaagccgt ctgcccaggc cccatctgac 120 actcttgaca tctgcaggtc ccagacccta tgatgtgtcc actctggagg ctcctcatct 180 tcctcgggtt gctggccttg cccttggcac cacacaagca gccttggcct ggcctggccc 240 aagcccacag agacaacaaa tccaccctgg caagaattat tgctcagggc ctcataaagc 300 acaacgcaga aagccgaatt cagaacatcc actttgggga cagactgaat gcctcagcac 360 aagtggcccc agggctggtg ggctggctaa tcagcggcag gaaacaccag cagcagcaag 420 agagcagcat caacatcacc aacattcagc tggactgtgg tgggatccag atatcattcc 480 ataaggagtg gttctcggca aatatctcac ttgaatttga ccttgaattg agaccgtcct 540 tcgataacaa catcgtaaag atgtgtgcac atatgagcat cgttgtggag ttctggctgg 600 agaaagacga gtttggccgg agggatctgg tgataggcaa atgcgatgca gagcccagca 660 gtgtccatgt ggccatcctc actgaggcta tcccaccaaa gatgaatcag tttctctaca 720 acctcaaaga gaatctgcaa aaagttctcc cacacatggt agaaagtcag gtatgtcctc 780 tgatcggtga aatcctcggg cagctggatg tgaaactgtt gaaaagcctc atagaacagg 840 aggctgctca tgaaccaacc caccatgaaa ccagccaacc ctcgtgcatg ccaggctgga 900 gagtccccca gctgacttct gctgatcaga aggaaagtcc acatcttgca accttaagtc 960 tcccttagag tggggcttct gctaccctaa aaactttacc ccaggctctg tggacatacc 1020 atcctctcct acaataaact ctagctctg 1049 30 2520 DNA Homo sapiens misc_feature Incyte ID No 6937367CB1 30 tgcccgccgg cccttccgcc tcactcagcg gcgccactga gagggacggg cgccagccat 60 ggagcgcaca gcaggcaaag agctggccct ggcaccgctg caggactggg gtgaagagac 120 cgaggacggc gcggtgtaca gtgtctccct gcggcggcag cgcagtcagc gcaggagccc 180 ggcggagggc cccgggggca gccaggctcc cagccccatt gccaatacct tcctccacta 240 tcgaaccagc aaggtgaggg tgctgagggc agcgcgcctg gagcggctgg tgggagagtt 300 ggtgtttgga gaccgtgagc aggaccccag cttcatgccc gccttcctgg ccacctaccg 360 gacctttgta cccactgcct gcctgctggg ctttctgctg ccaccaatgc caccgccccc 420 acctcccggg gtagagatca agaagacagc ggtacaagat ctgagcttca acaagaacct 480 gagggctgtg gtgtcagtgc tgggctcctg gctgcaggac caccctcagg atttccgaga 540 ccaccctgcc cattcggacc tgggcagtgt ccgaaccttt ctgggctggg cggccccagg 600 gagtgctgag gctcaaaaag cagagaagct tctggaagat tttttggagg aggctgagcg 660 agagcaggaa gaggagccgc ctcaggtgtg gacaggacct cccagagttg cccaaacttc 720 tgacccagac tcttcagagg cctgcgcgga ggaagaggaa gggctcatgc ctcaaggtcc 780 ccagctcctg gacttcagcg tggacgaggt ggccgagcag ctgaccctca tagacttgga 840 gctcttctcc aaggtgaggc tctacgagtg cttgggctcc gtgtggtcgc agagggaccg 900 gccgggggct gcaggcgcct cccccactgt gcgcgccacc gtggcccagt tcaacaccgt 960 gaccggctgt gtgctgggtt ccgtgctcgg agcaccgggc ttggccgccc cgcagagggc 1020 gcagcggctg gagaagtgga tccgcatcgc ccagcgctgc cgagaactgc ggaacttctc 1080 ctccttgcgc gccatcctgt ccgccctgca atctaacccc atctaccggc tcaagcgcag 1140 ctggggggca gtgagccggg aaccgctatc tactttcagg aaactttcgc agattttctc 1200 cgatgagaac aaccacctca gcagcagaga gattcttttc caggaggagg ccactgaggg 1260 atcccaagaa gaggacaaca ccccaggcag cctgccctca aaaccacccc caggccctgt 1320 cccctacctt ggcaccttcc ttacggacct ggttatgctg gacacagccc tgccggatat 1380 gttggagggg gatctcatta actttgagaa gaggaggaag gagtgggaga tcctggcccg 1440 catccagcag ctgcagaggc gctgtcagag ctacaccctg agcccccacc cgcccatcct 1500 ggctgccctg catgcccaga accagctcac cgaggagcag agctaccggc tctcccgggt 1560 cattgagcca ccagctgcct cctgccccag ctccccacgc atccgacggc ggatcagcct 1620 caccaagcgt ctcagtgcga agcttgcccg agagaaaagc tcatcaccta gtgggagtcc 1680 cggggacccc tcatccccca cctccagtgt gtccccaggg tcacccccct caagtcctag 1740 aagcagagat gctcctgctg gcagtccccc ggcctctcca gggccccagg gccccagcac 1800 caagctgccc ctgagcctgg acctgcccag cccccggccc ttcgctttgc ctctgggcag 1860 ccctcgaatc cccctcccgg cgcagcagag ctcggaggcc cgtgtcatcc gcgtcagcat 1920 cgacaatgac cacgggaacc tgtatcgaag catcttgctg accagtcagg acaaagcccc 1980 cagcgtggtc cggcgagcct tgcagaagca caatgtgccc cagccctggg cctgtgacta 2040 tcagctcttt caagtccttc ctggggaccg ggtgctcctg attcctgaca atgccaacgt 2100 cttctatgcc atgagtccag tcgcccccag agacttcatg ctgcggcgga aagaggggac 2160 ccggaacact ctgtctgtct ccccaagctg aggcagccct gtcctctcca caagacacaa 2220 gtcccacagg caagcttgcg actcttctcc tggaaagctg ccatccccca gtagaggcca 2280 ctgtgctgtg tatcccagga ccaccaccca actgtagccc attggacccc atctcttttt 2340 ctgactctgt tggtactaga tccatattcc aaagacatca gcccatgggt ggctggtgga 2400 gagctcaatc ccacaaatgt agaaagaggt ggggcatgga tacgtcaaat ccctccctag 2460 agaaatctta taaatgttag agacgcatca gaagtgacac atgcggatga actatgacat 2520 31 4360 DNA Homo sapiens misc_feature Incyte ID No 3876510CB1 31 gagatgacaa tagggagaat ggagaacgtg gaggtcttca ccgctgaggg caaaggaagg 60 ggtctgaagg ccaccaagga gttctgggct gcagatatca tctttgctga gcgggcttat 120 tccgcagtgg tttttgacag ccttgttaat tttgtgtgcc acacctgctt caagaggcag 180 gagaagctcc atcgctgtgg gcagtgcaag tttgcccatt actgcgaccg cacctgccag 240 aaggatgctt ggctgaacca caagaatgaa tgttcggcca tcaagagata tgggaaggtg 300 cccaatgaga acatcaggct ggcggcgcgc atcatgtgga gggtggagag agaaggcacc 360 gggctcacgg agggctgcct ggtgtccgtg gacgacttgc agaaccacgt ggagcacttt 420 ggggaggagg agcagaagga cctgcgggtg gacgtggaca cattcttgca gtactggccg 480 ccgcagagcc agcagttcag catgcagtac atctcgcaca tcttcggagt gattaactgc 540 aacggtttta ctctcagtga tcagagaggc ctgcaggccg tgggcgtagg catcttcccc 600 aacctgggcc tggtgaacca tgactgttgg cccaactgta ctgtcatatt taacaatggc 660 aatcatgagg cagtgaaatc catgtttcat acccagatga gaattgagct ccgggcccta 720 ggcaagatct cagaaggaga ggagctgact gtgtcctata ttgacttcct caacgttagt 780 gaagaacgca agaggcagct gaagaagcag tactactttg actgcacatg tgaacactgc 840 cagaaaaaac tgaaggatga cctcttcctg ggggtgaaag acaaccccaa gccctctcag 900 gaagtggtga aggagatgat acaattctcc aaggatacat tggaaaagat agacaaggct 960 cgttccgagg gtttgtatca tgaggttgtg aaattatgcc gggagtgcct ggagaagcag 1020 gagccagtgt ttgctgacac caacatctac atgctgcgga tgctgagcat tgtttcggag 1080 gtcctttcct acctccaggc ctttgaggag gcctcgttct atgccaggag gatggtggac 1140 ggctatatga agctctacca ccccaacaat gcccaactgg gcatggccgt gatgcgggca 1200 gggctgacca actggcacgc tggtaacatt gaggtggggc acgggatgat ctgcaaagcc 1260 tatgccattc tcctggtgac acacggaccc tcccacccca tcactaagga cttagaggcc 1320 atgcgggtgc agacggagat ggagctacgc atgttccgcc agaacgaatt catgtactac 1380 aagatgcgcg aggctgccct gaacaaccag cccatgcagg tcatggccga gcccagcaat 1440 gagccatccc cagctctgtt ccacaagaag caatgaggac tgcccagtgg aggaggggcg 1500 atgtggctgg ggagctaggg agagactctg gaggtggtgg gtctctgggg agacccctaa 1560 tgaggaagtt gaggtaatgc ttaacattgt tgctgtgaga atttactgcc ctgtgtttcc 1620 cagagccatt ttggctcaat tcaagtctat tcaattcaag ttaactctag cccagcccag 1680 atcaactcct cctacaaata ttattggatg ataggcccta gaacccaata aaggagctcc 1740 aaatgtcgtt gggtggggaa gcaaaatgta gagaaacatt taaagcacac tgtaataata 1800 aatgcaatta taaactatat ggaggagggt gcagaggagg gaatgtgtct ggtgtgtgat 1860 gtgtgtgtgt gcagtggggg tatcacagag agtatgacat ctgagttgag ggtagcaggt 1920 gcctggagtc tcaggtggct gctcacccat ctgtgcaggt gtctctgggg ctgctggtct 1980 cacctgtggt ctgcagtaga cacaattggc tgagcaggat atgtgatact gtgtggttgg 2040 tgtggagttt tgaagaaggg gctgtgtttg ggccacgtag gctctactca gagacctgaa 2100 accacttcag aatggtgcat atgtcgaaag agctggctgg gggccttgcc caaaccaact 2160 gaggtcttaa agtccgggga aaaaaagtct gggttccaac tagaattcta gaaatatttc 2220 tagaacacac agagagggaa taagtccctc tatcaccctt attaccaagc cttgtggttc 2280 cctgtgattt tagataatgt ctgatatttt tctggctatt tgcctagtag gatttaaaaa 2340 atattttcaa agtgaagctg agagagaatc ttggaaacac acatacctgt tgatcatggg 2400 ccctgcagaa ttggcccttg ggggctttat ttggttacat gtgcctgggt ggtctttacc 2460 agcttagact ctatcatggg cccccatgaa gctccattct caatactgaa taattattac 2520 ttcccttgtt gagtttcttt ttctgtcatg ccctgggggc ttctgctctt ctcaccagaa 2580 agaacatttg aatctggatt cttgtacacc tgggttagac cctgttcaga ggtgtggcca 2640 atttatcccg atctcctgga aggctgttgt gatttccatc taagaaatga gggtcttgag 2700 aatcaaccag tcccaagatt agcctgttat cctgttatct actgagacct caaatttctc 2760 accaatgttt tgggagatcc tggaaaagat cccttcagtt tggggtgtca ccaagacttc 2820 tacacaaccc aggactacca ttgacctcag agctgtaccc cacatcttga agtaaattga 2880 tcccaccagg tcccacgttt gttatctctg cctaaatgtt agcttctcca tcctcaccac 2940 atgatgacct gctgtgtccc tctgagcact acccagtggc tgaaaactct gcaaatgggc 3000 cacacttttg caaaatactt gtatctgaca cttaggtctt gtttgaagaa tttcctttct 3060 ggaaggtttt acaagaagac tgatagtctt tcaagccccc acatcacagg cttagggacg 3120 gcactaactt tctcccaggg atctaactgg ctagttcaaa ttatcactct tttaccttca 3180 tataaaatgt ctcccccaaa cctttttccc ttctttgtca ttgttatctg ctaagccact 3240 ggtcatttcc ccatattcgt agtctttttt tccatcctat ctttctaata tttgttgtct 3300 ttaacaaact gtgttctgtg tctgtgctcc tccttccctc tcagaccact ggaatgcaag 3360 tccttcttcc ctttggaatg tactctggat cccttcccct gctttgaccc ccagactttg 3420 ctccatctat tattgcttct ccatcctgga tccttgacat ttgtcacccc actggccttc 3480 tcaggtgcaa tcagtaaaaa tgctgagaac tcttggatct taatcttcat gactgagttt 3540 tttttagttg tatagttatc atctgccttt cttcactttg catttcttct tgaatccatt 3600 gcagattgac ttccactccc actccttcac taaaagggct cttaccaaga tcaaatctaa 3660 tgggtacatt ttagttccta tgtgatttgg cctttcgatg tcaatcatca ctcccagcca 3720 ttgattttgg tgacccactt ccctgtgatg atcttctgat ctagtttctc aggttccttc 3780 gctggtcctt tttctttccc tgcccctgac atattgacat ttcctggagt tggttttgtc 3840 cttgattcat tctcatgtca ttctgcacac agtctctgca tgaactcagg cagacccttc 3900 atttaatgac caccttaggg ctgatgattc tcaaatctgt attccccgat cttgcatttg 3960 agctccagcc ccactcatcc tctcggatgt tctgcaggcc cagcaaactc atcatgtcca 4020 aagtgaaact ttttctcttt cctgtctcct ctcctctgat ctgttctttc ttggaacacc 4080 acccaagaac gtcacctcct ccatcagatt gtgagctcct ggagggcagg agctgtgtcc 4140 ttctattcat cttcctatcc ccagaacctt gcacagatcc tggaatgtgg taggtgctca 4200 gtaaatgtgt gttgaataaa tgaatgaatg aatgaacaaa tgaatgaatt tgcttacttc 4260 aaggcaaaag aaccatgaaa ctgtattttg agtttctatg ttatagcagt cagcaaatcc 4320 tattaaatac tttgtgtttc caagcaaaaa aaaaaaaaaa 4360 32 3500 DNA Homo sapiens misc_feature Incyte ID No 4900076CB1 32 atcccgggca cgctggctct ggtgagcgcg gcctccgcgg ctccttggcc ccaggatgcc 60 ctctctcgtg gggaaaggag ggtcgggaaa ggccgagcgt aggtccacct tctccaatcc 120 ctgcctgctg ggagaggacg atctcttgag aaaggaaaga cttctgtgct cccgagaact 180 tcctatcagg tcctggctgc agggaaacaa gctgggcttt ttataattaa ggttggaaga 240 agtcaccaca ggcagcagaa ctccatcttg agatgaaata acatctacct ggacctctgg 300 cagaatttca aggcacacac tgggctgact ctggcgccat gatgttgcct tatccttcag 360 cactgggaga tcaatactgg gaagagattt tgcttccaaa gaatggggaa aatgtagaga 420 ctatgaagaa attgacccaa aatcataaag cgaaaggctt gccttctaat gatactgact 480 gcccccagaa aaaggaggga aaggcccaaa tagtggtacc agttacattc agggatgtga 540 ctgtgatctt cacagaagca gaatggaaga gactgagtcc agagcagagg aatctataca 600 aagaagtgat gctggagaat tacaggaatc ttctctcatt ggcagaacca aagccagaaa 660 tctacacttg ttcctcctgc cttctggcct tctcctgtca gcagttcctc agtcaacatg 720 tacttcagat cttcctgggc ttatgtgcag aaaatcactt ccatccaggg aattctagcc 780 cagggcattg gaaacagcag gggcagcagt attcccatgt aagctgttgg tttgaaaatg 840 cagaaggtca ggagagagga ggtggctcca aaccctggtc tgcaaggaca gaggagagag 900 aaacctcaag ggcattcccc agcccactcc aaagacagtc agcaagtcct agaaaaggca 960 acatggtggt agaaacagag cccagctcag cccaaagacc aaaccctgtg cagctagaca 1020 aaggcttgaa ggaattagaa accttgagat ttggagcaat caactgtaga gagtatgaac 1080 cggaccataa cctggaatca aactttatta caaacccgag gaccctctta gggaagaagc 1140 cctacatttg cagtgattgt gggcgaagct ttaaagatag atcaaccctc atcagacacc 1200 atcgtataca ctcgatggag aagccttatg tgtgcagtga gtgcgggcga ggttttagcc 1260 agaagtccaa cctcagcaga caccagagaa cacattcaga agagaagcct tatttgtgca 1320 gggagtgtgg gcaaagcttt agaagtaagt ccatcctcaa tagacatcag tggactcact 1380 cagaggagaa gccctatgtt tgcagcgagt gtgggcgagg ctttagcgag aagtcatcct 1440 tcatcagaca ccagaggaca cactccggtg agaaacccta tgtgtgcctg gagtgtggac 1500 gaagcttttg tgataagtca accctcagaa aacaccagag gatacactca ggggagaagc 1560 cttatgtttg cagggagtgt gggcgaggct ttagccagaa ctcagatctc atcaaacacc 1620 agaggacaca cttggatgag aagccttatg tttgcaggga gtgtgggcga ggcttttgtg 1680 acaagtcaac cctcatcata cacgagcgga cgcactctgg agagaagcct tatgtgtgtg 1740 gtgagtgtgg ccgaggcttt agtcggaaat cactcctcct tgtccaccag aggacacact 1800 caggggagaa gcattatgtc tgcagggagt gtaggcgagg ttttagccag aagtcaaatc 1860 tcatcagaca ccagaggacg cactcaaatg agaagcctta tatttgcagg gaatgtgggc 1920 gaggcttttg tgacaagtca accctcattg tacatgagag gacacactca ggagagaagc 1980 cttacgtgtg cagtgagtgt ggccgaggct ttagccggaa atcactcctc cttgtccacc 2040 agaggacaca ctcaggggag aagcattatg tttgtaggga gtgtgggcga ggctttagtc 2100 ataagtcaaa tctcatcaga caccagagga cacactgacg ggagaaacct gtgtatgcag 2160 gggtcatgaa caagacctga gtgaccagtc aagcctcatg ttaccccaga gagacacatg 2220 gggagtagac cctgtgtaca cagattgtga gtgaagttcc agagatgtgt cagcccttat 2280 caggcatggg agggacacgt tcaggagagg agccttatga gtatagagta cgggcaactg 2340 tagccatcag tcggccttga gcatgcacaa aaggacacac ttaggagaga agtttatgtg 2400 tagggactgt gggaaggctt tagcaataat caacatttac cagacatcca atgacagcct 2460 caggggaaag cacccttgtc tggggagtgt tggggagcat cagtaaaaga atggacactc 2520 aggcacagag tggccctcag gaaggaggtc tttgtttgta ggatgtatgg gcaaagcttt 2580 tgtgatcaca caccacaggg agaatctgca tgtggggaca ctgtggagct ctgcccagat 2640 gaccttttca ggggtaacac cccagctgct tgagagaaca gtgttgctgc tggcagagat 2700 gcattccaga gatgcactcc gctctggaac tcactctcag ccacagggag ctgcatgcac 2760 cacaggggca atgcaccttt gcaggggtac cttctggccc caacccttga ctcaacgggg 2820 acaactccag aaggtcattc cagatccaga gatccccatc gaactgaagg atcactgggt 2880 tgcagacaca ttgcaggtca gcttcttcct ctgcccagtc ctgccctcac tccccagtga 2940 atcctcaatt ttctgtctcg ttgtctgtcc agataattga ttctaagaca tgttaggtat 3000 ataaggagtg tagataaggc ttcagccatg agtcaccccc cagtaagccc cagagtatat 3060 tgaatagaaa ttctgcatgt gtggggagaa tggacaagga cttaggaaaa agtcctcatc 3120 aaagaacagc ttttttggga caagctttac atgggtgggg agggaaaatg tgaaacacat 3180 tagcaataag ttaaacctca tcttgtacta aaggaggaca cactcaggga gaagacctct 3240 gtgggcaggg cttgtgggtg gagcttcatc ccgatgtcac tcctcaactg acttaggagg 3300 acagtcttgc taccccaagt cactacctca ctcacctctg agggattttc aggaaatgtc 3360 ttgactcccc catgtactct gtatgtgagc gaagatggca gtaactgtta aataagcatt 3420 cttttctact tcttggaatc agatgaaata aaaaagcagg ctttatttaa gtaatcaaaa 3480 aaaaaaaaaa aaaaaaaaaa 3500 33 1366 DNA Homo sapiens misc_feature Incyte ID No 1543848CB1 33 ttcggagggt cgcagcgcgg tagatcgcaa tacagggcct tgaaaatcga gaatttcctg 60 caaggcccac acgcctgcaa gggaaccggg cccggaggaa ttaaatttcc cggggtgaac 120 gagaggctcg gctaattcgg cggccccccc tttttttttt tttttttttt tttttcggct 180 cgagcccttg ggcggtggtg gaggtggtaa ccgtgatagt agcagctccg gcggcagcaa 240 cagcgactac gagggatggc ggcggctgca gcaggaactg caacatccca gaggtttttc 300 cagagcttct cggatgccct aatcgacgag gacccccagg cggcgttaga ggagctgact 360 aaggctttgg aacagaaacc agatgatgca cagtattatt gtcaaagagc ttattgtcac 420 attcttcttg ggaattactg tgttgctgtt gctgatgcaa agaagtctct agaactcaat 480 ccaaataatt ccactgctat gctgagaaaa ggaatatgtg aataccatga aaaaaactat 540 gctgctgccc tagaaacttt tacagaagga caaaaattag atatagagac ggggtttcat 600 cgtgttggcc aggctggtct ccaactcttg acctcaagtg atccacctgc cttggactcc 660 caaagtgctg ggattacagg tgcagatgct aatttcagtg tctggattaa aaggtgtcaa 720 gaagctcaga atggctcaga atctgaggtg tggactcatc agtcaaaaat caagtatgac 780 tggtatcaaa cagaatctca agtagtcatt acacttatga tcaagaatgt tcagaagaat 840 gatgtaaatg tggaattttc agaaaaagag ttgtctgctt tggttaaact tccttctgga 900 gaggattaca atttgaaact ggaacttctt catcctataa taccagaaca gagcacgttt 960 aaagtacttt caacaaagat tgaaattaaa ctgaaaaagc cagaggctgt gagatgggaa 1020 aagctagagg ggcaaggaga tgtgcctacg ccaaaacaat tcgtagcaga tgtaaagaac 1080 ctatatccat catcatctcc ttatacaaga aattgggata aattggttgg tgagatcaaa 1140 gaagaagaaa agaatgaaaa gttggaggga gatgcagctt taaacagatt atttcagcag 1200 atctattcag atggttctga tgaagtgaaa cgtgccatga acaaatcctt tatggagtcg 1260 ggtggtacag ttttgagtac caactggtct gatgtaggta aaaggaaagt tgaaatcaat 1320 cctcctgatg atatggaatg gaaaaagtac taaataaatt aaattc 1366 34 4524 DNA Homo sapiens misc_feature Incyte ID No 6254070CB1 34 gtggccgcag cgggttcctg agtgaattac ccaggaggga ctgagcacag caccaactag 60 aggggggcca ggggtgcggg actcgagcga gcaggaagga ggcagcgcct ggcaccaggg 120 ctttgactca acagaattga gacacgtttg taatcgctgg cgtgccccgc gcacaggatc 180 ccagcgaaat cagatttcct ggtgaggttg cgtgggtgga ttaatttgga aaaagaaact 240 gcctatatct tgccatcaaa aaactcacgg aggagaagcg cagtcaatca acagtaaact 300 taagagtccc cggatgcttc cgttgtttaa acttgtatgc ttgaaaatta tctgagaggc 360 aataaacatc tgctcctttc ttccctctcc agaagtccat tggaatatta agcccaggag 420 ttgcttgggg atggctggaa gtgcaatgtc ttccaagttc ttcctagtgg ctttggccat 480 atttttctcc ttcgcccagg ttgtaattga agccaattct tggtggtcgc taggtatgaa 540 taaccctgtt cagatgtcag aagtatatat tataggagca cagcctctct gcagccaact 600 ggcaggactt tctcaaggac agaagaaact gtgccacttg tatcaggacc acatgcagta 660 catcggagaa ggcgcgaaga caggcatcaa agaatgccag tatcaattcc gacatcgaag 720 gtggaactgc agcactgtgg ataacacctc tgtttttggc agggtgatgc agataggcag 780 ccgcgagacg gccttcacat acgcggtgag cgcagcaggg gtggtgaacg ccatgagccg 840 ggcgtgccgc gagggcgagc tgtccacctg cggctgcagc cgcgccgcgc gccccaagga 900 cctgccgcgg gactggctct ggggcggctg cggcgacaac atcgactatg gctaccgctt 960 tgccaaggag ttcgtggacg cccgcgagcg ggagcgcatc cacgccaagg gctcctacga 1020 gagtgctcgc atcctcatga acctgcacaa caacgaggcc ggccgcagga cggtgtacaa 1080 cctggctgat gtggcctgca agtgccatgg ggtgtccggc tcatgtagcc tgaagacatg 1140 ctggctgcag ctggcagact tccgcaaggt gggtgatgcc ctgaaggaga agtacgacag 1200 cgcggcggcc atgcggctca acagccgggg caagttggta caggtcaaca gccgcttcaa 1260 ctcgcccacc acacaagacc tggtctacat cgaccccagc cctgactact gcgtgcgcaa 1320 tgagagcacc ggctcgctgg gcacgcaggg ccgcctgtgc aacaagacgt cggagggcat 1380 ggatggctgc gagctcatgt gctgcggccg tggctacgac cagttcaaga ccgtgcagac 1440 ggagcgctgc cactgcaagt tccactggtg ctgctacgtc aagtgcaaga agtgcacgga 1500 gatcgtggac cagtttgtgt gcaagtagtg ggtgccaccc agcactcagc cccgctccca 1560 ggacccgctt attatagaaa gtacagtgat tctggttttt ggtttttaga aatatttttt 1620 atttttcccc aagaattgca accggaacca ttttttttcc tgttaccatc taagaactct 1680 gtggtttatt attaatatta taattattat ttggcaataa tgggggtggg aaccaagaaa 1740 aatatttatt ttgtggatct ttgaaaaggt aatacaagac ttcttttgat agtatagaat 1800 gaagggggaa ataacacata ccctaactta gctgtgtggg acatggtaca catccagaag 1860 gtaaagaaat acattttctt tttctcaaat atgccatcat atgggatggg taggttccag 1920 ttgaaagagg gtggtagaaa tctattcaca attcagcttc tatgaccaaa atgagttgta 1980 aattctctgg tgcaagataa aaggtcttgg gaaaacaaaa caaaacaaaa caaacctccc 2040 ttccccagca gggctgctag cttgctttct gcattttcaa aatgataatt tacaatggaa 2100 ggacaagaat gtcatattct caaggaaaaa aggtatatca catgtctcat tctcctcaaa 2160 tattccattt gcagacagac cgtcatattc taatagctca tgaaatttgg gcagcaggga 2220 ggaaagtccc cagaaattaa aaaatttaaa actcttatgt caagatgttg atttgaagct 2280 gttataagaa ttgggattcc agatttgtaa aaagaccccc aatgattctg gacactagat 2340 tttttgtttg gggaggttgg cttgaacata aatgaaatat cctgtatttt cttagggata 2400 cttggttagt aaattataat agtagaaata atacatgaat cccattcaca ggtttctcag 2460 cccaagcaac aaggtaattg cgtgccattc agcactgcac cagagcagac aacctatttg 2520 aggaaaaaca gtgaaatcca ccttcctctt cacactgagc cctctctgat tcctccgtgt 2580 tgtgatgtga tgctggccac gtttccaaac ggcagctcca ctgggtcccc tttggttgta 2640 ggacaggaaa tgaaacatta ggagctctgc ttggaaaaca gttcactact tagggatttt 2700 tgtttcctaa aacttttatt ttgaggagca gtagttttct atgttttaat gacagaactt 2760 ggctaatgga attcacagag gtgttgcagc gtatcactgt tatgatcctg tgtttagatt 2820 atccactcat gcttctccta ttgtactgca ggtgtacctt aaaactgttc ccagtgtact 2880 tgaacagttg catttataag gggggaaatg tggtttaatg gtgcctgata tctcaaagtc 2940 ttttgtacat aacatatata tatatataca tatatataaa tataaatata aatatatctc 3000 attgcagcca gtgatttaga tttacagctt actctggggt tatctctctg tctagagcat 3060 tgttgtcctt cactgcagtc cagttgggat tattccaaaa gttttttgag tcttgagctt 3120 gggctgtggc cccgctgtga tcataccctg agcacgacga agcaacctcg tttctgagga 3180 agaagcttga gttctgactc actgaaatgc gtgttgggtt gaagatatct ttttttcttt 3240 tctgcctcac ccctttgtct ccaacctcca tttctgttca ctttgtggag agggcattac 3300 ttgttcgtta tagacatgga cgttaagaga tattcaaaac tcagaagcat cagcaatgtt 3360 tctcttttct tagttcattc tgcagaatgg aaacccatgc ctattagaaa tgacagtact 3420 tattaattga gtccctaagg aatattcagc ccactacata gatagctttt tttttttttt 3480 ttttttttta ataaggacac ctctttccaa acaggccatc aaatatgttc ttatctcaga 3540 cttacgttgt tttaaaagtt tggaaagata cacatctttt catacccccc cttaggaggt 3600 tgggctttca tatcacctca gccaactgtg gctcttaatt tattgcataa tgatatccac 3660 atcagccaac tgtggctctt taatttattg cataatgata ttcacatccc ctcagttgca 3720 gtgaattgtg agcaaaagat cttgaaagca aaaagcacta attagtttaa aatgtcactt 3780 ttttggtttt tattatacaa aaaccatgaa gtactttttt tatttgctaa atcagattgt 3840 tcctttttag tgactcatgt ttatgaagag agttgagttt aacaatccta gcttttaaaa 3900 gaaactattt aatgtaaaat attctacatg tcattcagat attatgtata tcttctagcc 3960 tttattctgt acttttaatg tacatatttc tgtcttgcgt gatttgtata tttcactggt 4020 ttaaaaaaca aacatcgaaa ggcttatgcc aaatggaaga tagaatataa aataaaacgt 4080 tacttgtata ttggtaaaaa aaaaaaaaaa aaaaaaaaaa aaaaaaaaaa aaaaaaaaaa 4140 aaaaaaaaaa aaaaaaaaaa aacaaaaaaa aaaaaaaaca aaaaacccaa gaaaataaca 4200 tcagccggcg gcgcgcccca gtggggggca gccacagggc tcccttttaa gagcttctag 4260 aaagaggcgg gagagaacca ggggacacta gagtgagtgc agcggggaaa aaagtgtttc 4320 ccgggccaaa tgcccacaca ttatctgaga agtgaaagtt gaaaacgcca caaaattccc 4380 acaagaatac gcacagggag gggaacaaaa caagaacaga agaggaacac agacagaagc 4440 ggaaagagcc aagaaggagc cgaaaaaaac cgcaaaagga caccgcccgg cggcagcgga 4500 accgccagag acaggacaca cgct 4524 35 1157 DNA Homo sapiens misc_feature Incyte ID No 1289839CB1 35 tggagttgga cctggagaaa agtcaagtca taagtcaaga aagattgggc cctactactg 60 gaatgcagga aaaaatggag gagggatgga gaggtttgga aaggcagcca caggggttct 120 gggagaggga aggcattcta agtggcagta acagcttcag caaagtccca aaggtggaaa 180 agtgcaggac acgtccaggg ataagccagt gcactaagcc cacctcttgt ccccacagtc 240 caggtggagg ccgcagaggg cccagggcaa gcagaggcag caatggttgg tcctgacggt 300 ggctgagccc ccagcccctg gaatatgcag cccgggggag ccccagacag cggcaaggac 360 gaggtggcgg agtggggcgg gaggcatggt ctccacctac cgggtggccg tgctgggggc 420 gcgaggtgtg ggcaagagtg ccatcgtgcg ccagttcttg tacaacgagt tcagcgaggt 480 ctgcgtcccc accaccgccc gccgccttta cctgcctgct gtcgtcatga acggccacgt 540 gcacgacctc cagatcctcg actttccacc catcagcgcc ttccctgtca atacgctcca 600 ggagtgggca gacacctgct gcaggggact ccggagtgtc cacgcctaca tcctggtcta 660 cgacatctgc tgctttgaca gctttgagta cgtcaagacc atccgccagc agatcctgga 720 gacgagggtg atcggaacct cagagacgcc catcatcatc gtgggcaaca agcgggacct 780 gcagcgcgga cgcgtgatcc cgcgctggaa cgtgtcgcac ctggtacgca agacctggaa 840 gtgcggctac gtggaatgct cggccaagta caactggcac atcctgctgc tcttcagcga 900 gctgctcaag agcgtcggct gcgcccgttg caagcacgtg cacgctgccc tgcgcttcca 960 gggcgcgctg cgccgcaacc gctgcgccat catgtgacgc ctgcgcgccc ctcgggctgc 1020 accggcactg gccgagcgga gggcggggcc gtactgcggg gctggggcgg ggagcgggcg 1080 ggaaatggaa ctgtgacggt cccggcctga ggcccctgca gccacgcacc tcccggtgag 1140 aagcagagcg cgagagg 1157 36 1418 DNA Homo sapiens misc_feature Incyte ID No 5565648CB1 36 ggacgcctgc tcagtgcgcg ccggccgggc aaccctatgc tggcgtaatc gggttcctcc 60 gagccgccgt aggactggtt ccggcgggct ggtgaggaat ggagccggta ggctgctgcg 120 gcgagtgccg cggctcctcc gtagacccgc ggagcacctt cgtgttgagt aacctggcgg 180 aggtggtgga gcgtgtgctc accttcctgc ccgccaaggc gttgctgcgg gtggcctgcg 240 tgtgccgctt atggagggag tgtgtgcgca gagtattgcg gacccatcgg agcgtaacct 300 ggatctccgc aggcctggcg gaggccggcc acctggaggg gcattgcttg gttcgcgtgg 360 tagcagagga gcttgagaat gttcgcatct taccacatac agttctttac atggctgatt 420 cagaaacttt cattagtctg gaagagtgtc gtggccataa gagagcaagg aaaagaacta 480 gtatggaaac agcacttgcc cttgagaagc tattccccaa acaatgccaa gtccttggga 540 ttgtgacccc aggaattgta gtgactccaa tgggatcagg tagcaatcga cctcaggaaa 600 tagaaattgg agaatctggt tttgctttat tattccctca aattgaagga ataaaaatac 660 aaccctttca ttttattaag gatccaaaga atttaacatt agaaagacat caactcactg 720 aagtaggtct tttagataac cctgaacttc gtgtggtcct tgtctttggt tataattgct 780 gtaaggtggg agccagtaat tatctgcagc aagtagtcag cactttcagt gatatgaata 840 tcatcttggc tggaggccag gtggacaacc tgtcatcact gacttctgaa aagaaccctc 900 tggatattga tgcctcgggt gtggttggac tgtcatttag tggacaccga atccagagtg 960 ccactgtgct cctcaacgag gacgtcagtg atgagaagac tgctgaggct gcgatgcagc 1020 gcctcaaagc ggccaacatt ccagagcata acaccattgg cttcatgttt gcatgcgttg 1080 gcaggggctt tcagtattac agagccaagg ggaatgttga ggctgatgca tttagaaagt 1140 tttttcctag tgttccctta ttcggcttct ttggaaatgg agaaattgga tgtgatcgga 1200 tagtcactgg gaactttata ttgaggaaat gtaatgaggt aaaagatgat gatctgtttc 1260 atagctatac aacaataatg gcactcatac atctggggtc atctaaataa taattaaagt 1320 ggctttcata atatgtaact tttgggttct gcctttttca gaaaatggaa acttgggcca 1380 tgtgtatttt caacaaaaat actttagata tatctttt 1418 37 4113 DNA Homo sapiens misc_feature Incyte ID No 2764456CB1 37 tgctttatta accactctag gtattattct aacactttat gtgcctatta aattatcccg 60 acatattaga tttgctgaat tgcagtccat atttcgtaga tatgatagct gaagcacgga 120 atcattaggt aacttgccca aagtggcatt cacgactcat aaatggctta ggatgtaaac 180 tcagttttat tccctgggac gccctctctg ctcttcagca cttgaagttc aggcagcgag 240 agttgacatg gggccaggct gcgcccctgg ggcgggttga agacagggtg agtctcttga 300 tattcaggaa atcatcgcgc acccagtcac cagcgttcgg gagcctgtcg cagcgggacc 360 gacggaatcc ggagcaggcg acagggcgca gaagcgggat gtacttctgt tggggcgccg 420 actccaggga gctgcagcgc cggaggacgg cgggcagccc cggggctgag ctactgcagg 480 cggccagcgg ggagcgccac tctctgctgc tgctgaccaa ccacagggtc ctctcgtgcg 540 gagacaacag caggggtcag ctgggccgca ggggcgcgca gcgcggggag ctgccagaac 600 caattcaggc attggaaacc ctaattgttg atctcgtgag ctgcgggaag gagcactccc 660 tggctgtgtg ccacaaagga agggtcttcg catggggagc tggttctgaa gggcagctgg 720 ggattggaga attcaaggaa ataagtttca cacctaagaa aataatgact ctgaatgata 780 taaaaataat acaagtttcc tgtggacact accactccct ggcattatca aaagatagcc 840 aagtgttttc gtggggaaag aacagccatg ggcagctggg cttggggaag gagttcccct 900 cccaagccag cccgcagagg gtgaggtccc tggaggggat cccactggct caggtggctg 960 ccggaggggc tcacagcttt gccctgtctc tctgtgggac ttcgtttggc tggggaagta 1020 acagtgccgg gcagctggcc ctcagtgggc gtaatgtccc agtgcaaagc aacaagcctc 1080 tctcagtcgg tgcactgaag aatctaggtg tggtttatat cagctgtggt gatgcacaca 1140 ctgcggtgct tacccaggac gggaaagtgt tcacatttgg agacaatcgc tctggacagc 1200 tgggatacag ccccactcct gagaagagag gtccacaact tgtggaaaga attgatggcc 1260 tagtttcgca gatagattgt ggaagttatc acaccctggc atatgtgcac accactggtc 1320 aggtggtatc ttttggtcat ggaccaagtg acacaagcaa gccaactcat ccggaggccc 1380 tgacagagaa ctttgacatt agctgcctga tttctgctga agacttcgtg gatgttcaag 1440 tcaaacacat ttttgctgga acatatgcca actttgtgac aactcatcag gatactagtt 1500 ccacacgtgc tcccgggaaa accctgccag aaataagccg aattagccag tccatggcag 1560 aaaaatggat agcagtgaaa agaagaagta ctgaacatga aatggctaaa agtgaaatta 1620 gaatgatatt ttcatctcct gcttgtctga ctgcaagttt tttaaagaaa agaggaactg 1680 gagaaacgac ttccattgat gtggacttag aaatggcaag agataccttc aagaagttaa 1740 caaaaaagga atggatttct tccatgataa ctacgtgtct cgaggatgat ctgctcagag 1800 ctcttccatg ccattctcca caccaagaag ctttatcagt tttcctcctg ctcccagaat 1860 gtcctgtgat gcatgattct aagaactgga agaacctggt ggttccattt gcaaaggctg 1920 tgtgtgaaat gagtaaacaa tctttgcaag tcctaaagaa gtgttgggca tttttgcaag 1980 aatcttctct gaatccgctg atccagatgc ttaaagcagc catcatctct cagctgcttc 2040 atcagactaa aaccgaacag gatcactgta atgttaaagc tcttttagga atgatgaaag 2100 aactgcataa ggtaaacaaa gctaactgtc gactaccaga aaatactttc aacataaatg 2160 aactctccaa cttattaaac ttttatatag atagaggaag acagctcttt cgggataacc 2220 acctgatacc tgcagaaacc cccagtcctg ttattttcag tgattttcca tttatcttta 2280 attcgctatc caaaattaaa ttattgcaag ctgattcaca tataaagatg cagatgtcag 2340 aaaagaaagc atacatgctt atgcatgaaa caattctgca aaaaaaggat gaatttcctc 2400 catcacccag atttatactt agagtcagac gaagtcgcct ggttaaagat gctctgcgtc 2460 aattaagtca agctgaagct actgacttct gcaaagtatt agtggttgaa tttattaatg 2520 aaatttgtcc tgagtctgga ggggttagtt cagagttctt ccactgtatg tttgaagaga 2580 tgaccaagcc agaatatgga atgttcatgt atcctgaaat gggttcctgc atgtggtttc 2640 ctgccaagcc taaacctgag aagaaaagat atttcctctt tggaatgctg tgtggactct 2700 ccttattcaa tttaaatgtt gctaaccttc ctttcccact ggctctgtat aaaaaacttc 2760 tggaccaaaa gccatcattg gaagatttaa aagaactcag tcctcggttg gggaagagtt 2820 tgcaagaagt tctagatgat gctgctgatg acattggaga tgcgctctgc atacgctttt 2880 ctatacactg ggaccaaaat gatgttgact taattccaaa tgggatctcc atacctgtgg 2940 accaaaccaa caagagagac tatgtttcta agtatattga ttacattttc aacgtctctg 3000 taaaagcagt ttatgaggaa tttcagagag gattttatag agtctgtgag aaggagatac 3060 ttagacattt ctaccctgaa gaactaatga cagcaatcat tggaaatact gattatgact 3120 ggaaacagtt tgaacagaat tcaaagtatg agcaaggata ccaaaaatca catcctacta 3180 tacagttgtt ttggaaggct ttccacaaac taaccttgga tgaaaagaaa aaattcctct 3240 ttttccttac aggacgtgat aggctgcatg caagaggcat acagaaaatg gaaatagtat 3300 ttcgctgtcc tgaaactttc agtgaaagag atcacccaac atcaataact tgtcataata 3360 ttctctccct ccctaagtat tctacaatgg aaagaatgga ggaagcactt caagtagcca 3420 tcaacaacaa cagaggattt gtctcaccca tgctcacaca gtcataatca cctctgagag 3480 actcagggtg ggctttctca cacttggatc cttctgttct tccttacacc taaataatac 3540 aagagattaa tgaatagtgg ttagaagtag ttgagggaga gattggggga atggggagat 3600 gatgatgatg gtcaaagggt gcaaaatctc acacaagact gaggcaggag aatagggtac 3660 agagataggg atctaaggat gacttggaca cactccctgg cactgaagag tctgaacact 3720 ggcctgtgat tggtccattc caggaccttc atttgcataa ggtatcaaac cacatcagcc 3780 tctgattggc catgggccag acctgcactc tggccaatga ttggttcatt ccaggacatt 3840 catttgcata aggagtcaaa ccacaccagt cttggattgg ctgtgagcca attcacctca 3900 gtctctaatt ggctgtgagt cagtctttca tttacatagg gtgtaaccat caagaaacct 3960 ctacagggta cttaagcccc agaagatttt gctaccaggg ctcttgagcc acttgctcta 4020 gcccactccc accctgtgga atgtactttc acttttgctg cttcactgcc ttgtgctcca 4080 ataaatccac tccttcacca cccaaaaaaa aaa 4113 38 7058 DNA Homo sapiens misc_feature Incyte ID No 5734806CB1 38 cgttccgtta gcggcgtggg gttggctgca gtggcagtgc tttctcttct gctcacgggg 60 acccgctcag gctggaggcc agccagctct tgccgccacc tcggtcgcga tgggggcgca 120 ggaccggccg cagtgccact tcgacatcga gatcaaccgg gagccggttg gtcgcattat 180 gtttcagctc ttctcagaca tatgtccaaa aacatgcaaa aacttccttt gcttgtgctc 240 aggagagaaa ggccttggga aaacaactgg gaagaagtta tgttataaag gttctacgtt 300 ccatcgtgtg gttaaaaact ttatgattca gggtggggac ttcagtgaag gtaatggaaa 360 aggtggagaa tcaatttatg gtggatattt taaagatgaa aactttattc tcaaacatga 420 cagagcgttc cttttatcaa tggcaaatcg agggaaacat accaatggtt cccagttttt 480 cataacaaca aagcctgctc cacacctgga tggggtgcat gtagtctttg gactggttat 540 ttctggtttt gaagtaatcg aacaaattga aaatctgaag accgatgctg caagcagacc 600 atatgcagat gtgcgagtta ttgactgtgg agtacttgcc acaaaatcaa taaaagatgt 660 ttttgagaaa aaaaggaaga aaccaactca ttcagaaggc tcggattcct cttccaattc 720 ctcctcttct tcagaatcat cttcagaaag tgaacttgaa catgagagaa gcagaaggag 780 gaaacataag aggaggccaa aagttaaacg ttctaaaaag aggcgaaagg aagcaagcag 840 ttcagaagag ccaaggaata aacatgcaat gaacccaaaa ggtcactctg agaggagtga 900 taccaatgaa aaaaggtcag ttgattccag tgctaaaagg gaaaaacctg tggtccgccc 960 agaagagatt cctccagtgc ctgagaaccg atttttactg agaagagata tgcctgttgt 1020 tactgcagaa cctgaaccaa ttcctgatgt tgcacccatt gtaagtgatc agaaaccatc 1080 tgtatcaaag tctggacgga agattaaagg aaggggcaca attcgctatc acacacctcc 1140 aagatcaaga tcctgttctg agtcagatga tgatgacagc agtgaaactc ctcctcactg 1200 gaaagaggaa atgcagagat taagagcata tagaccacct agtggagaaa aatggagtaa 1260 aggagataag ttaagtgacc cctgttcaag ccgatgggat gaaagaagct tgtctcagag 1320 atccagatca tggtcctata atggatatta ttcagacctt agtacagcaa gacactctgg 1380 ccaccataaa aaacgcagaa aagaaaaaaa ggttaagcat aaaaagaaag ggaaaaagca 1440 gaaacactgc agaagacaca aacaaacaaa gaagagaagg attcttatac cgtctgacat 1500 agaatcctca aaatcttcca ctcgaagaat gaaatcctct tgtgatagag aaaggagttc 1560 tcgttcttcc tcattgtcat ctcatcactc atcaaagaga gactggtcta aatctgataa 1620 ggatgtccag agctctttaa cccattccag cagagactca tacagatcaa aatctcactc 1680 acagtcttat tctagaggaa gctcaagatc aaggactgcg tcaaagtcct catcacattc 1740 tcgaagtaga tcaaagtcca gatctagttc caagtctggg caccgaaaga gagcatcaaa 1800 atcaccaaga aaaacagctt ctcagttaag tgaaaataaa ccagttaaaa cagaaccttt 1860 aagagcaacc atggcacaaa atgaaaatgt agtagtacaa ccagttgtag cagaaaatat 1920 tcctgtaata ccactgagtg acagtccccc cccttcaaga tggaagcctg gacagaaacc 1980 ttggaagccc tcttatgagc gaattcagga aatgaaagct aaaacaaccc atttgctacc 2040 catccaaagc acttacagtt tagcaaatat taaagagact ggtagctcat catcctacca 2100 taaaagagaa aaaaattcgg aaagtgatca gagcacttat tcaaaataca gtgatagaag 2160 ttcagaaagc tcaccaaggt caaggagcag atcttctagg agtagatctt attccagatc 2220 atatacaaga tcacgtagtc tagctagttc acattcaagg tctaggtctc catcatctag 2280 atctcattca cgaaataaat acagtgatca ttcacagtgt agtagatcat cttcatatac 2340 ttctattagc agtgatgatg gaaggcgagc taagaggaga cttagatcca gtgggaaaaa 2400 aaatagcgtt tcacataaaa agcatagcag cagctctgaa aagacacttc acagtaaata 2460 tgtcaaaggt agagacaggt cttcatgtgt gagaaagtat agcgagagca gatcatcttt 2520 agattattct tcagacagtg agcagtcaag tgttcaggcc acacagtcag cccaggaaaa 2580 agagaagcag ggccaaatgg aaagaacaca taataaacaa gaaaaaaaca gaggtgaaga 2640 aaaatccaag tctgaacggg aatgccctca ttcaaaaaaa agaactttga aagagaatct 2700 ttctgatcac cttagaaatg gcagtaagcc caaaaggaag aattatgctg gtagtaaatg 2760 ggactctgag tcaaattcag aacgagatgt cactaaaaac agtaaaaatg actcccatcc 2820 atcctctgac aaggaagaag gtgaggccac atccgattct gaatcagagg ttagtgaaat 2880 tcacatcaaa gtcaaaccca caaccaagtc gtccacaaat acttcactgc ctgatgataa 2940 tggtgcttgg aaatcaagca aacagcgcac atcaacttct gactctgagg ggtcctgttc 3000 caattcggaa aacaataggg gaaagccaca aaagcacaaa catgggtcaa aggaaaatct 3060 taaaagagaa cacaccaaaa aagtgaaaga gaaattgaaa gggaaaaaag acaaaaagca 3120 taaggctcca aaacgaaagc aagcatttca ctggcagcct ccactagaat ttggtgaaga 3180 ggaggaggag gagattgatg acaagcaagt tactcaggaa tcaaaagaga aaaaagtttc 3240 tgaaaacaat gaaaccataa aagataatat tctaaaaact gagaaatcca gtgaagagga 3300 cctttcaggt aaacatgata cagtgactgt ttcatcagat cttgatcagt ttactaaaga 3360 tgatagtaaa ctcagtattt ctcccacagc tttaaatact gaggaaaatg tggcctgttt 3420 acaaaacatt cagcacgttg aagaaagtgt tcccaatgga gtggaagatg tgcttcaaac 3480 agatgacaac atggagatct gcactcctga taggagttcc ccagcaaaag tagaggagac 3540 ttcccctcta ggaaatgcac ggcttgatac cccagatata aacattgttt tgaagcagga 3600 tatggcaacg gaacatcctc aagcagaggt agtaaaacag gaaagcagca tgtccgaaag 3660 taaagtgttg ggtgaagtgg ggaaacagga cagcagctct gctagcttgg ctagtgctgg 3720 agaaagtacc gggaagaagg aggtggctga gaagagccag atcaacctca ttgataagaa 3780 atggaagccc ctgcaaggtg tggggaacct ggcagcacct aatgctgcca catccagtgc 3840 tgtggaagtt aaggtgttga ccactgtgcc tgaaatgaaa ccacaaggct tgagaataga 3900 aattaaaagc aaaaataaag ttcggcctgg gtctctcttt gatgaagtaa gaaagacagc 3960 acgcttaaac cgtagaccaa gaaatcagga gagttcaagt gatgagcaga cgcctagtcg 4020 ggatgatgat agccagtcca ggagtccaag tagatctcga agtaaatctg aaaccaaatc 4080 aagacacaga acaaggtctg tctcctatag tcactcaaga agtcgatcga gaagttccac 4140 atcatcttat cgatcaagaa gctactctag aagtcggagc agaggatggt acagcagagg 4200 ccgaaccaga agccggagca gttcctaccg gagttacaaa agtcacagga cgtccagcag 4260 gagcagatcc aggagcagct catatgatcc ccacagtcga tccagcaggt cctacaccta 4320 cgatagctac tatagcagga gtcggagtcg aagtagaagc cagagaagtg acagttacca 4380 ccgaggcaga agttataatc ggcggtccag gagttgtaga tcttatggct ctgacagtga 4440 aagtgaccga agttactctc atcaccggag ccccagtgag agcagcagat acagttgaaa 4500 acgtccggat acaaattata tcttatttgt aaatatctgg caacttagct taagaaatgt 4560 aatgacagtc tgttgttcta tttcaatatc agaggtgaat ttcaaaaata gacacttctt 4620 aattgttact ggttcattta catgtgggga gaagaattta aaatacagat atgtctccta 4680 aaaatatttt tatgccacat tttacagtag ccaactatgg aaatgaattt cattttcttg 4740 aatcaagaaa tcgtgaaatt tatctatgta taatttgcaa tattatttta agtctatttc 4800 actctatctt acgtatccct tagaatacag attctttttg cctgtttttc cagttttagc 4860 atatatgctg ccaagcatag aactgtgaag gagaactgtt aaaggcggcc aaatatttat 4920 atactgatta catagagtct tgtacatatg tgctctaaaa acaaaccacc cagaattgat 4980 actgttggta accaggagta taaggcagtg gctctggggt tcttaattca ttcctaactt 5040 ctttgatact tcacaggatt aggaaagtgg tcatcataca tcccacacag tctgtattac 5100 ttcaggcttg tgggcaaggt taggaagaat caatcagcct taactataaa tacctgcact 5160 gtctctgagg acttactatt ttatgttctt tttaatcaat accgatcaga agtttaggtt 5220 ataaaaacaa ttctacttca tgctttggtg cttggtaatt tttggtgcgt ctttaagcat 5280 tactcttata tatcatatat taaaatacca taaaaatgaa attcagacaa aatcactggc 5340 accaaaaatg gtttattctg agctgtcttc actttgacta tttggggggc ttctctcaag 5400 tacagatgtg ggttggggtc ccctggagca ggcaggattg gcagtaagag atattggcca 5460 ctcaagtcta ctgtgtgtgt gtgcctctgg aagagtgaag aatggacttc aaaagtaaca 5520 tcaaaaatct aactgccacc atcctggaga cattttgcag ggctttcctt tcaagtcttt 5580 caagtacagg atattaccac aacagcagct gaactgttgt aaccagcatg tttttcctat 5640 ttccactgtg acctgcagct gactcaaagc cttgcgtgac ctgacccagg tgcaagagac 5700 aggggaagag ggatagaggg tatagcataa attacatatt ttcatggctt tgggtggttc 5760 ctccaaaaat aattggacct gtaaaaacta gtgtgtgtgt gtgtgtgtgt gtgtgtgtgt 5820 gtgtggtttt tttttttaat ctttactttg aatttgttcc ccaagtgtac ttaatcacct 5880 tagtgccagt ttaatccagt tatgcagaag aaattcatat tggttgcctg atgtagagct 5940 cagcaccacc ctaccacagg ccttgtctgg tgtatttggg aagtggaaaa gagccctcag 6000 ttggagggag ctgacaaccc ttggtggagg gagggtgccc ttgaatgtat taaaactatc 6060 acccaaagaa ggtatgaaaa cagggtaagg tggtcagttg tttgccaggt caatagacag 6120 aaagtacatt agaaaacagg acttaggcca aacaaacaat actggatact gaatacaaaa 6180 cagtatgatt tatattaaag gtttccaaag gttgcctgca aaggagaata ttactactag 6240 tcagcaggaa aaaaatgcat tcagaaccca agcagaaact gccaaatgta attaggttaa 6300 gaaaagttac ccttgggcag tgtattagtt ttctattgct gtgtgacaaa ttaccccaaa 6360 tttagcagtt taaaaaacaa tacccatagc agttctgtag ctcatgagtc tggcacagtg 6420 tggctggatt ctctgctcag ggtcttaaag gctgaaataa gggttggcag gacaacattc 6480 cttcatggag gctctgggga agaatctgct tctaagttca ttcaggttgt tggcggaatt 6540 cagttctttg ctggctctca gctggaggcc cctctctcac ctcaaggctg cctgcattcc 6600 ttcttatgtg gtcccctcca gcttcaaacc agccttcctg ctctttctca tgcttcatat 6660 ctctctcccg tcctcctgtt ttaggggcat atgattagct caagcccaca gatatatttt 6720 aaggttgatt gtgcgataga acataattgc aggagtactg tctcatctca tcatattcac 6780 gggttctgga gattagctca ttgaaagtgg gaggggcatt ttcaaattct gcctaccaca 6840 ggcaataact gcccatctca gctgtaggtg gaatttttac ccagaaaaga taggccctag 6900 aagcctcatt tcttttctcc atggaaaagg acagccctct gctgcagcgt tcaacttgtg 6960 tgtttactga cagagtgaac tacagaaata gcttttcttc ctaaagggga ttgttctaca 7020 ttttgaagtt attttttaat aaaattgaat tatgttgt 7058 39 1380 DNA Homo sapiens misc_feature Incyte ID No 7495168CB1 39 agggccggtc ttgcagagta gctgcggtga gtgggcgtgt gcgccgagcg gtctggccca 60 agggctgggg gccggccgag ggtcttcggg agcaggccgc agggcgcgga gagatcctgg 120 gatcgccgtc cgccgctgct acccggcatg tcggcggagg cctcgggccc ggctgccgcc 180 gcggccccgt ccctggaagc ccccaagccc tcgggtctcg agcctggccc cgccgcctac 240 ggtctcaagc cgctgacccc gaacagcaaa tacgtgaagc tgaacgtggg cggctcgttg 300 cactacacca cgctgcgcac cctcacggga caggacacca tgctcaaagc catgttcagc 360 ggccgcgtgg aggtgctgac cgatgccgga ggttgggtgc tgattgaccg gagcggccgt 420 cactttggta caatcctcaa ttacctgcgg gatgggtctg tgccactgcc ggagagtacg 480 agagaactgg gggagctgct gggcgaagca cgctactacc tggtgcaggg cctgattgag 540 gactgccagc tggcgctgca gcaaaaaagg gagacgctgt ccccgctgtg cctcatcccc 600 atggtgacat ctccccggga ggagcagcag ctcctggcca gcacctccaa gcccgtggtg 660 aagctcctgc acaaccgcag taacaacaag tactcctaca ccagcacttc agatgacaac 720 ctacttaaga acatcgagct gttcgacaag ctggccctgc gcttccacgg gcggctactc 780 ttcctcaagg atgtcctggg ggacgagatc tgctgctggt ctttctacgg gcagggccgc 840 aaaatcgccg aggtgtgctg cacctccatt gtctatgcta cggagaagaa gcagaccaag 900 gtggaatttc cagaggcccg gatcttcgag gagaccctga acatcctcat ctacgagact 960 ccccggggcc cagacccagc cctcctggag gccacagggg gagcagctgg agctggtggg 1020 gctggccgcg gggaggatga agagaaccga gagcaccgtg tccgcaggat ccatgtccgg 1080 cgccatatca cccacgacga gcgtcctcat ggccaacaaa ttgtcttcaa ggactgacct 1140 ctgaccctcc ccctgccttc ctcttgcctt gggacccagt ccctctctct ttccctcccc 1200 ttcccagact tttgccccgg ctctgctggc caagtcgtgg gtcctcctct gtcccttcat 1260 tgcatggcac agctcacttg gcccttctcc acccatccca accccatgct aacaacatgg 1320 tacattcgcc ccaccacttt cagccagcat atacatcttg tttctcgctt gtttcttgtc 1380 40 1773 DNA Homo sapiens misc_feature Incyte ID No 7483131CB1 40 gcgcccacgg gccggctcag cggcggtggc ggcaggctgt ttttcttcaa ataaagaaca 60 tggtgaaact gattcacaca ttagctgatc atggtgacga tgtcaactgc tgtgccttct 120 ccttttccct cttggctact tgctccttgg acaaaacaat tcgcctgtac tcgttacgtg 180 actttactga actgccacat tctccattga agtttcatac ctatgctgtc cactgctgct 240 gtttctcccc ttcaggacat attttggcat cgtgttcaac agatggtacc actgtcctat 300 ggaatactga aaatggacag atgctggcag tgatggaaca gcctagtggc agccctgtga 360 gggtttgcca gttttcccca gactccacgt gtttggcatc aggggcagct gatggaactg 420 tggttttgtg gaatgcacag tcatacaaat tatatagatg tggtagtgtt aaagatggct 480 ccttggcggc atgtgcattt tctcctaatg gaagcttctt tgtcactggc tcctcatgtg 540 gtgatttaac agtgtgggat gataaaatga ggtgtctgca tagtgaaaaa gcacatgatc 600 ttggaattac ctgctgcgat ttttcttcac agccagtttc tgatggagaa caaggtcttc 660 agttttttcg actggcatca tgtggtcagg attgccaagt caaaatttgg attgtttctt 720 ttacccatat cttaggtttt gaattaaaat ataaaagtac actgagtggg cactgtgctc 780 ctgttctggc ttgtgctttt tcccatgatg ggcagatgct agtctcaggg tcagtggata 840 agtctgtcat agtatatgat actaatactg agaatatact tcacacattg actcagcaca 900 ccaggtatgt cacaacttgt gcttttgcac ctaataccct tttacttgct actggttcaa 960 tggacaaaac agtgaacatc tggcaatttg acctggaaac actttgccaa gcaaggagca 1020 cagaacatca gctgaagcaa tttaccgaag attggtcaga ggaggatgtc tcaacatggc 1080 tttgtgcaca agatttaaaa gatcttgttg gtattttcaa gatgaataac attgatggaa 1140 aagaactgtt gaatcttaca aaagaaagtc tggctgatga tttgaaaatt gaatctctag 1200 gactgcgtag taaagtgctg aggaaaattg aagagctcag gaccaaggtt aaatcccttt 1260 cttcaggaat tcctgatgaa tttatatgtc caataactag agaacttatg aaagatccgg 1320 tcatcgcatc agatggctat tcatatgaaa aggaagcaat ggaaaattgg atcagcaaaa 1380 agaaacgtac aagtcccatg acaaatcttg ttcttccttc agcggtactt acaccaaata 1440 ggactctgaa aatggccatc aatagatggc tggagacaca ccaaaagtaa aattgttgat 1500 attgtattat ttatattttc agtgatctca tttgaatgat ttataggtaa atactaatca 1560 gacattatta aaagcaaaac aggaaaaagg taaacttctt aaatttagtt acctataaaa 1620 attgtcaatt ttcattcttt aaaaacacat ggacttacta taaaagcctt tttgtactag 1680 tgaaaagaat cttcagctat atagaaataa agttatactt taaattgcaa aaaaaaaaaa 1740 aaaaaaaatt ctcggccgca atgaattcgt ggc 1773 41 2810 DNA Homo sapiens misc_feature Incyte ID No 4558650CB1 41 actgcccact tatgcactga gccttccgga gggacgagtc tacaggggtc gcgcgtcgta 60 acgacgtcac ttccgtcgga aggttctcat gaggagccac tcagattcct gtcacttctc 120 aaagcatctc cgtcgtgaac atggccctgc caccattctt cggccagggt cgcccaggcc 180 caccgccccc gcagccgccg cctcctgctc ctttcggctg tccgccaccg ccgctgccct 240 ccccggcttt cccgccgcct ctcccccagc ggcccggccc ttttccgggg gcctccgccc 300 ccttccttca gcctccgctg gctctgcagc cccgagcctc cgcggaggcc tcccgcggcg 360 gaggcggcgc tggcgccttc tacccggtgc caccaccgcc gctgcctcct ccgccgcccc 420 agtgtcggcc cttcccgggg accgacgccg gcgagcggcc gcggccaccg cctcccggcc 480 cggggccgcc ctggagcccg cggtggcctg aggcgccgcc gccgccggcc gacgtgctcg 540 gggatgcggc cctccaacgc ctgcgcgacc ggcagtggct ggaggcggtg ttcgggaccc 600 cgcggcgggc aggctgtccg gtgccccagc gcacgcatgc cgggcccagc cttggcgaag 660 tgcgcgcgcg attgctccgg gctctgcgcc tggtgcggcg gctgcgcggc ctgagccagg 720 ccctgcgcga ggccgaagcc gacggcgcgg cctgggtcct gctgtactcc cagaccgcgc 780 cgctgcgcgc ggaactggcc gagcggctac agccgttgac ccaggctgcc tatgtgggcg 840 aggcgcggag gaggctggag agggtccggc gccgccggct gcggcttcgc gagagggccc 900 gggaacgcga ggccgagcgg gaggcagagg ccgcgcgggc agtggaacgc gagcaggaga 960 ttgaccgctg gagggtgaag tgtgtgcagg aggtggagga gaagaagcgg gagcaggaac 1020 tcaaagcagc cgctgatggc gtactatctg aagtgaggaa aaaacaagca gataccaaaa 1080 gaatggtgga cattctacgg gctttggaga aattgaggaa actgaggaaa gaggctgcag 1140 cgaggaaagg ggtctgtcct ccagcctcag cagatgagac ttttacgcat catcttcagc 1200 gactgagaaa actcattaaa aagcgctctg aactgtatga agctgaagag agagccctca 1260 gagttatgct agaaggagaa caagaggaag agaggaaaag agaattagaa aagaaacaaa 1320 gaaaagagga agagaaaatt ttacttcaga aacgtgaaat tgagtccaag ttgtttgggg 1380 atccagatga gttcccactt gctcacctct tggagccttt ccgacagtat tatctccaag 1440 ccgagcactc cctgccagcg ctcatccaga tcaggcatga ttgggatcag tacctggtgc 1500 catccgatca tcccaaaggc aacttcgttc cccaaggatg ggtccttccc ccgctcccca 1560 gcaacgacat ctgggcaact gctgttaagc tgcattagta aagatgctcc aggagtgtgg 1620 tccagccagc gctctttcca gctgtaaata ttagcgatgg tgccatcttt tgctgtagac 1680 taaactgcaa cttctaaatt ccatgtggca ttcccctacc ctgaagttat gctttccttc 1740 tgtgctctgt gctggccaga ggtgcctctt gaatcagatt aatgtggttt ttcaggaaag 1800 gacttaggtg aactgaggtt tttaccacag gcagtgaatg accttggttc accaaatttg 1860 cctctgtttt gaggggcttg gtccagagtg acttgttaat ttactctaac ttccttgtgt 1920 gttgatgggt aagtacactc aaacactgaa tacaggtgtg tgatgggtag atttcacagc 1980 ccttctacta atagtgagtg tgaaggcaag cttgatgcaa aacctcctga cctttcctac 2040 ctgaagagcc ctttgacttc taggaagaaa ggtcaaaaat gttatcttca gttgtgttaa 2100 tcccagtttt agtgcagctt aggaggctgc tagttaggaa gatggcagtg gctgtaggct 2160 gggttgccag aaaagatggt ggcctagtct tattattcag atggagaact tagaaaacct 2220 gaagagtacc caaattggat tgtattttaa tggacaatgg ctgtattttt tccatgttag 2280 aaggatccta atgaaagcac ctgttatttt taagtttcta agggtctagt tgttcagaat 2340 ccccaaggat atttccctaa cctcactcag tcacattgta ggagccagtg tagctatgga 2400 attatcttag gaactcaagc ttctaaaact atccatgtag tcaaatctag gggaaaaagc 2460 aaataaaaat agtaaaattt ggccgggcac agtggctcac gcctgtaatc ccaacacttt 2520 gggaggccga ggcgggccga tcacgaggtc aggagatcaa ggccatcctg gctaacacgg 2580 tgaaaccctg tctctactaa aaatacaaaa aaatattagc tgggcgtagg tggtgcacac 2640 ctgtagtccc agctactggg gaggctgagg caggagaatg gtgtaaaacc caggaggcag 2700 agcttgcagt gagccgagat cgcgccacgg cactccagcc tgggagacag agcaagactc 2760 cgtctcaaaa aaaaaaaagg taaaatttat tttttatatt cattaataaa 2810 42 2549 DNA Homo sapiens misc_feature Incyte ID No 7506195CB1 42 aggttgaacg actgcccact tatgcactga gccttccgga gggacgagtc tacaggggtc 60 gcgcgtcgta acgacgtcac ttccgtcgga aggttctcat gaggagccac tcagattcct 120 gtcacttctc aaagcatctc cgtcgtgaac atggccctgc caccattctt cggccagggt 180 cgcccaggcc caccgccccc gcagccgccg cctcctgctc ctttcggctg tccgccaccg 240 ccgctgccct ccccggcttt cccgccgcct ctcccccagc ggcccggccc ttttccgggg 300 gcctccgccc ccttccttca gcctccgctg gctctgcagc cccgagcctc cgcggaggcc 360 tcccgcggcg gaggcggcgc tggcgccttc tacccggtgc caccaccgcc gctgcctcct 420 ccgccgcccc agtgtcggcc cttcccgggg accgacgccg gcgagcggcc gcggccaccg 480 cctcccggcc cggggccgcc ctggagcccg cggtggcctg aggcgccgcc gccgccggcc 540 gacgtgctcg gggatgcggc cctccaacgc ctgcgcgacc ggcagtggct ggaggcggtg 600 ttcgggaccc cgcggcgggc aggctgtccg gtgccccagc gcacgcatgc cgggcccagc 660 cttggcgaag tgcgcgcgcg attgctccgg gctctgcgcc tggtgcggcg gctgcgcggc 720 ctgagccagg ccctgcgcga ggccgaagcc gacggcgcgg cctgggtcct gctgtactcc 780 cagaccgcgc cgctgcgcgc ggaactggcc gagcggctac agccgttgac ccaggctgcc 840 tatgtgggcg aggcgcggag gaggctggag agggtccggc gccgccggct gcggcttcgc 900 gagagggccc gggaacgcga ggccgagcgg gaggcagagg ccgcgcgggc agtggaacgc 960 gagcaggaga ttgaccgctg gagggtgaag tgtgtgcagg aggtggagga gaagaagcgg 1020 gagcaggaac tcaaagcagc cgctgatggc gtactatctg aagtgaggaa aaaacaagca 1080 gataccaaaa gaatggtgga cattctacgg gctttggaga aattgaggaa actgaggaaa 1140 gaggctgcag cgaggaaaga tgagttccca cttgctcacc tcttggagcc tttccgacag 1200 tattatctcc aagccgagca ctccctgcca gcgctcatcc agatcaggca tgattgggat 1260 cagtacctgg tgccatccga tcatcccaaa ggcaacttcg ttccccaagg atgggtcctt 1320 cccccgctcc ccagcaacga catctgggca actgctgtta agctgcatta gtaaagatgc 1380 tccaggagtg tggtccagcc agcgctcttt ccagctgtaa atattagcga tggtgccatc 1440 ttttgctgta gactaaactg caacttctaa attccatgtg gcattcccct accctgaagt 1500 tatgctttcc ttctgtgctc tgtgctggcc agaggtgcct cttgaatcag attaatgtgg 1560 tttttcagga aaggacttag gtgaactgag gtttttacca caggcagtga atgaccttgg 1620 ttcaccaaat ttgcctctgt tttgaggggc ttggtccaga gtgacttgtt aatttactct 1680 aacttccttg tgtgttgatg ggtaagtaca ctcaaacact gaatacaggt gtgtgatggg 1740 tagatttcac agcccttcta ctaatagtga gtgtgaaggc aagcttgatg caaaacctcc 1800 tgacctttcc tacctgaaga gccctttgac ttctaggaag aaaggtcaaa aatgttatct 1860 tcagttgtgt taatcccagt tttagtgcag cttaggaggc tgctagttag gaagatggca 1920 gtggctgtag gctgggttgc cagaaaagat ggtggcctag tcttattatt cagatggaga 1980 acttagaaaa cctgaagagt acccaaattg gattgtattt taatggacaa tggctgtatt 2040 ttttccatgt tagaaggatc ctaatgaaag cacctgttat ttttaagttt ctaagggtct 2100 agttgttcag aatccccaag gatatttccc taacctcact cagtcacatt gtaggagcca 2160 gtgtagctat ggaattatct taggaactca agcttctaaa actatccatg tagtcaaatc 2220 taggggaaaa agcaaataaa aatagtaaaa tttggccggg cacagtggct cacgcctgta 2280 atcccaacac tttgggaggc cgaggcgggc cgatcacgag gtcaggagat caaggccatc 2340 ctggctaaca cggtgaaacc ctgtctctac taaaaataca aaaaaatatt agctgggcgt 2400 aggtggtgca cacctgtagt cccagctact ggggaggctg aggcaggaga atggtgtaaa 2460 acccaggagg cagagcttgc agtgagccga gatcgcgcca cggcactcca gcctgggaga 2520 cagagcaaga ctccgtctca aaaaaaaaa 2549 

What is claimed is:
 1. An isolated polypeptide selected from the group consisting of: a) a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO:1-21, b) a polypeptide comprising a naturally occurring amino acid sequence at least 90% identical to an amino acid sequence selected from the group consisting of SEQ ID NO:3-4, SEQ ID NO:6, SEQ ID NO:8-9, SEQ ID NO:11-12, SEQ ID NO:14-16, SEQ ID NO:18-21, c) a polypeptide comprising a naturally occurring amino acid sequence at least 93% identical to the amino acid sequence of SEQ ID NO:1, d) a polypeptide comprising a naturally occurring amino acid sequence at least 95% identical to the amino acid sequence of SEQ ID NO:2, e) a polypeptide comprising a naturally occurring amino acid sequence at least 96% identical to the amino acid sequence of SEQ ID NO:5, f) a polypeptide comprising a naturally occurring amino acid sequence at least 98% identical to a polynucleotide sequence selected from the group consisting of SEQ ID NO:7 and SEQ ID NO:10, g) a polypeptide comprising a naturally occurring amino acid sequence at least least 99% identical to the polynucleotide sequence of SEQ ID NO:17, h) a biologically active fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO:1-21, and i) an immunogenic fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO:1-21.
 2. An isolated polypeptide of claim 1 comprising an amino acid sequence selected from the group consisting of SEQ ID NO:1-21.
 3. An isolated polynucleotide encoding a polypeptide of claim
 1. 4. An isolated polynucleotide encoding a polypeptide of claim
 2. 5. An isolated polynucleotide of claim 4 comprising a polynucleotide sequence selected from the group consisting of SEQ ID NO:22-42.
 6. A recombinant polynucleotide comprising a promoter sequence operably liked to a polynucleotide of claim
 3. 7. A cell transformed with a recombinant polynucleotide of claim
 6. 8. A transgenic organism comprising a recombinant polynucleotide of claim
 6. 9. A method of producing a polypeptide of claim 1, the method comprising: a) culturing a cell under conditions suitable for expression of the polypeptide, wherein said cell is transformed with a recombinant polynucleotide, and said recombinant polynucleotide comprises a promoter sequence operably linked to a polynucleotide encoding the polypeptide of claim 1, and b) recovering the polypeptide so expressed.
 10. A method of claim 9, wherein the polypeptide comprises an amino acid sequence selected from the group consisting of SEQ ID NO:1-21.
 11. An isolated antibody which specifically binds to a polypeptide of claim
 1. 12. An isolated polynucleotide selected from the group consisting of: a) a polynucleotide comprising a polynucleotide sequence selected from the group consisting of SEQ ID NO:22-42, b) a polynucleotide comprising a naturally occurring polynucleotide sequence at least 90% identical to a polynucleotide sequence selected from the group consisting of SEQ ID NO:22-25, SEQ ID NO:27, SEQ ID NO:29, SEQ ID NO:30, SEQ ID NO:32-37, SEQ ID NO:39-42, c) a polynucleotide comprising a naturally occurring polynucleotide sequence at least 92% identical to the polynucleotide sequence of SEQ ID NO:26, d) a polynucleotide comprising a naturally occurring polynucleotide sequence at least 98% identical to a polynucleotide sequence selected from the group consisting of SEQ ID NO:28 and SEQ ID NO:31, e) a polynucleotide comprising a naturally occurring polynucleotide sequence at least 99% identical to the polynucleotide sequence of SEQ ID NO:38, f) a polynucleotide complementary to a polynucleotide of a), g) a polynucleotide complementary to a polynucleotide of b), h) a polynucleotide complementary to a polynucleotide of c), i) a polynucleotide complementary to a polynucleotide of d), j) a polynucleotide complementary to a polynucleotide of e), and k) an RNA equivalent of a)-j).
 13. An isolated polynucleotide comprising at least 60 contiguous nucleotides of a polynucleotide of claim
 12. 14. A method of detecting a target polynucleotide in a sample, said target polynucleotide having a sequence of a polynucleotide of claim 12, the method comprising: a) hybridizing the sample with a probe comprising at least 20 contiguous nucleotides comprising a sequence complementary to said target polynucleotide in the sample, and which probe specifically hybridizes to said target polynucleotide, under conditions whereby a hybridization complex is formed between said probe and said target polynucleotide or fragments thereof, and b) detecting the presence or absence of said hybridization complex, and, optionally, if present, the amount thereof.
 15. A method of claim 14, wherein the probe comprises at least 60 contiguous nucleotides.
 16. A method of detecting a target polynucleotide in a sample, said target polynucleotide having a sequence of a polynucleotide of claim 12, the method comprising: a) amplifying said target polynucleotide or fragment thereof using polymerase chain reaction amplification, and b) detecting the presence or absence of said amplified target polynucleotide or fragment thereof, and, optionally, if present, the amount thereof.
 17. A composition comprising a polypeptide of claim 1 and a pharmaceutically acceptable excipient.
 18. A composition of claim 17, wherein the polypeptide comprises an amino acid sequence selected from the group consisting of SEQ ID NO:1-21.
 19. A method for treating a disease or condition associated with decreased expression of functional CGDD, comprising administering to a patient in need of such treatment the composition of claim
 17. 20. A method of screening a compound for effectiveness as an agonist of a polypeptide of claim 1, the method comprising: a) exposing a sample comprising a polypeptide of claim 1 to a compound, and b) detecting agonist activity in the sample.
 21. A composition comprising an agonist compound identified by a method of claim 20 and a pharmaceutically acceptable excipient.
 22. A method for treating a disease or condition associated with decreased expression of functional CGDD, comprising administering to a patient in need of such treatment a composition of claim
 21. 23. A method of screening a compound for effectiveness as an antagonist of a polypeptide of claim 1, the method comprising: a) exposing a sample comprising a polypeptide of claim 1 to a compound, and b) detecting antagonist activity in the sample.
 24. A composition comprising an antagonist compound identified by a method of claim 23 and a pharmaceutically acceptable excipient.
 25. A method for treating a disease or condition associated with overexpression of functional CGDD, comprising administering to a patient in need of such treatment a composition of claim
 24. 26. A method of screening for a compound that specifically binds to the polypeptide of claim 1, the method comprising: a) combining the polypeptide of claim 1 with at least one test compound under suitable conditions, and b) detecting binding of the polypeptide of claim 1 to the test compound, thereby identifying a compound that specifically binds to the polypeptide of claim
 1. 27. A method of screening for a compound that modulates the activity of the polypeptide of claim 1, the method comprising: a) combining the polypeptide of claim 1 with at least one test compound under conditions permissive for the activity of the polypeptide of claim 1, b) assessing the activity of the polypeptide of claim 1 in the presence of the test compound, and c) comparing the activity of the polypeptide of claim 1 in the presence of the test compound with the activity of the polypeptide of claim 1 in the absence of the test compound, wherein a change in the activity of the polypeptide of claim 1 in the presence of the test compound is indicative of a compound that modulates the activity of the polypeptide of claim
 1. 28. A method of screening a compound for effectiveness in altering expression of a target polynucleotide, wherein said target polynucleotide comprises a sequence of claim 5, the method comprising: a) exposing a sample comprising the target polynucleotide to a compound, under conditions suitable for the expression of the target polynucleotide, b) detecting altered expression of the target polynucleotide, and c) comparing the expression of the target polynucleotide in the presence of varying amounts of the compound and in the absence of the compound.
 29. A method of assessing toxicity of a test compound, the method comprising: a) treating a biological sample containing nucleic acids with the test compound, b) hybridizing the nucleic acids of the treated biological sample with a probe comprising at least 20 contiguous nucleotides of a polynucleotide of claim 12 under conditions whereby a specific hybridization complex is formed between said probe and a target polynucleotide in the biological sample, said target polynucleotide comprising a polynucleotide sequence of a polynucleotide of claim 12 or fragment thereof, c) quantifying the amount of hybridization complex, and d) comparing the amount of hybridization complex in the treated biological sample with the amount of hybridization complex in an untreated biological sample, wherein a difference in the amount of hybridization complex in the treated biological sample is indicative of toxicity of the test compound.
 30. A diagnostic test for a condition or disease associated with the expression of CGDD in a biological sample, the method comprising: a) combining the biological sample with an antibody of claim 11, under conditions suitable for the antibody to bind the polypeptide and form an antibody:polypeptide complex, and b) detecting the complex, wherein the presence of the complex correlates with the presence of the polypeptide in the biological sample.
 31. The antibody of claim 11, wherein the antibody is: a) a chimeric antibody, b) a single chain antibody, c) a Fab fragment, d) a F(ab′)₂ fragment, or e) a humanized antibody.
 32. A composition comp rising an antibody of claim 11 and an acceptable excipient.
 33. A method of diagnosing a condition or disease associated with the expression of CGDD in a subject, comprising administering to said subject an effective amount of the composition of claim
 32. 34. A composition of claim 32, wherein the antibody is labeled.
 35. A method of diagnosing a condition or disease associated with the expression of CGDD in a subject, comprising administering to said subject an effective amount of the composition of claim
 34. 36. A method of preparing a polyclonal antibody with the specificity of the antibody of claim 11, the method comprising: a) immunizing an animal with a polypeptide consisting of an amino acid sequence selected from the group consisting of SEQ ID NO:1-21, or an immunogenic fragment thereof under conditions to elicit in antibody response, b) isolating antibodies from said animal, and c) screening the isolated antibodies with the polypeptide, thereby identifying a polyclonal antibody which specifically binds to a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO:1-21.
 37. A polyclonal antibody produced by a method of claim
 36. 38. A composition comprising the polyclonal antibody of claim 37 and a suitable carrier.
 39. A method of making a monoclonal antibody with the specificity of the antibody of claim 11, the method comprising: a) immunizing an animal with a polypeptide consisting of an amino acid sequence selected from the group consisting of SEQ ID NO:1-21, or an immunogenic fragment thereof, under conditions to elicit an antibody response, b) isolating antibody producing cells from the animal, c) fusing the antibody producing cells with immortalized cells to form monoclonal antibody-producing hybridoma cells, d) culturing the hybridoma cells, and e) isolating from the culture monoclonal antibody which specifically binds to a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO:1-21.
 40. A monoclonal antibody produced by a method of claim
 39. 41. A composition comprising the monoclonal antibody of claim 40 and a suitable carrier.
 42. The antibody of claim 11, wherein the antibody is produced by screening a Fab expression library.
 43. The antibody of claim 11, wherein the antibody is produced by screening a recombinant immunoglobulin library.
 44. A method of detecting a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO:1-21 in a sample, the method comprising: a) incubating the antibody of claim 11 with a sample under conditions to allow specific binding of the antibody and the polypeptide, and b) detecting specific binding, wherein specific binding indicates the presence of a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO:1-21 in the sample.
 45. A method of purifying a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO:1-21 from a sample, the method comprising: a) incubating the antibody of claim 11 with a sample under conditions to allow specific binding of the antibody and the polypeptide, and b) separating the antibody from the sample and obtaining the purified polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO:1-21.
 46. A microarray wherein at least one element of the microarray is a polynucleotide of claim
 13. 47. A method of generating an expression profile of a sample which contains polynucleotides, the method comprising: a) labeling the polynucleotides of the sample, b) contacting the elements of the microarray of claim 46 with the labeled polynucleotides of the sample under conditions suitable for the formation of a hybridization complex, and c) quantifying the expression of the polynucleotides in the sample.
 48. An array comprising different nucleotide molecules affixed in distinct physical locations on a solid substrate, wherein at least one of said nucleotide molecules comprises a first oligonucleotide or polynucleotide sequence specifically hybridizable with at least 30 contiguous nucleotides of a target polynucleotide, and wherein said target polynucleotide is a polynucleotide of claim
 12. 49. An array of claim 48, wherein said first oligonucleotide or polynucleotide sequence is completely complementary to at least 30 contiguous nucleotides of said target polynucleotide.
 50. An array of claim 48, wherein said first oligonucleotide or polynucleotide sequence is completely complementary to at least 60 contiguous nucleotides of said target polynucleotide.
 51. An array of claim 48, wherein said first oligonucleotide or polynucleotide sequence is completely complementary to said target polynucleotide.
 52. An array of claim 48, which is a microarray.
 53. An array of claim 48, further comprising said target polynucleotide hybridized to a nucleotide molecule comprising said first oligonucleotide or polynucleotide sequence.
 54. An array of claim 48, wherein a linker joins at least one of said nucleotide molecules to said solid substrate.
 55. An array of claim 48, wherein each distinct physical location on the substrate contains multiple nucleotide molecules, and the multiple nucleotide molecules at any single distinct physical location have the same sequence, and each distinct physical location on the substrate contains nucleotide molecules having a sequence which differs from the sequence of nucleotide molecules at another distinct physical location on the substrate.
 56. A polypeptide of claim 1, comprising the amino acid sequence of SEQ ID NO:1.
 57. A polypeptide of claim 1, comprising the amino acid sequence of SEQ ID NO:2.
 58. A polypeptide of claim 1, comprising the amino acid sequence of SEQ D NO:3.
 59. A polypeptide of claim 1, comprising the amino acid sequence of SEQ ID NO:4.
 60. A polypeptide of claim 1, comprising the amino acid sequence of SEQ ID NO:5.
 61. A polypeptide of claim 1, comprising the amino acid sequence of SEQ ID NO:6.
 62. A polypeptide of claim 1, comprising the amino acid sequence of SEQ ID NO:7.
 63. A polypeptide of claim 1, comprising the amino acid sequence of SEQ ID NO:8.
 64. A polypeptide of claim 1, comprising the amino acid sequence of SEQ ID NO:9.
 65. A polypeptide of claim 1, comprising the amino acid sequence of SEQ ID NO:10.
 66. A polypeptide of claim 1, comprising the amino acid sequence of SEQ ID NO:11.
 67. A polypeptide of claim 1, comprising the amino acid sequence of SEQ ID NO:12.
 68. A polypeptide of claim 1, comprising the amino acid sequence of SEQ ID NO:13.
 69. A polypeptide of claim 1, comprising the amino acid sequence of SEQ ID NO:14.
 70. A polypeptide of claim 1, comprising the amino acid sequence of SEQ ID NO:15.
 71. A polypeptide of claim 1, comprising the amino acid sequence of SEQ ID NO:16.
 72. A polypeptide of claim 1, comprising the amino acid sequence of SEQ ID NO:17.
 73. A polypeptide of claim 1, comprising the amino acid sequence of SEQ ID NO:18.
 74. A polypeptide of claim 1, comprising the amino acid sequence of SEQ ID NO:19.
 75. A polypeptide of claim 1, comprising the amino acid sequence of SEQ ID NO:20.
 76. A polypeptide of claim 1, comprising the amino acid sequence of SEQ ID NO:21.
 77. A polynucleotide of claim 12, comprising the polynucleotide sequence of SEQ ID NO:22.
 78. A polynucleotide of claim 12, comprising the polynucleotide sequence of SEQ ID NO:23.
 79. A polynucleotide of claim 12, comprising the polynucleotide sequence of SEQ ID NO:24.
 80. A polynucleotide of claim 12, comprising the polynucleotide sequence of SEQ ID NO:25.
 81. A polynucleotide of claim 12, comprising the polynucleotide sequence of SEQ ID NO:26.
 82. A polynucleotide of claim 12, comprising the polynucleotide sequence of SEQ ID NO:27.
 83. A polynucleotide of claim 12, comprising the polynucleotide sequence of SEQ ID NO:28.
 84. A polynucleotide of claim 12, comprising the polynucleotide sequence of SEQ ID NO:29.
 85. A polynucleotide of claim 12, comprising the polynucleotide sequence of SEQ ID NO:30.
 86. A polynucleotide of claim 12, comprising the polynucleotide sequence of SEQ ID NO:31.
 87. A polynucleotide of claim 12, comprising the polynucleotide sequence of SEQ ID NO:32.
 88. A polynucleotide of claim 12, comprising the polynucleotide sequence of SEQ ID NO:33.
 89. A polynucleotide of claim 12, comprising the polynucleotide sequence of SEQ ID NO:34.
 90. A polynucleotide of claim 12, comprising the polynucleotide sequence of SEQ ID NO:35.
 91. A polynucleotide of claim 12, comprising the polynucleotide sequence of SEQ ID NO:36.
 92. A polynucleotide of claim 12, comprising the polynucleotide sequence of SEQ ID NO:37.
 93. A polynucleotide of claim 12, comprising the polynucleotide sequence of SEQ ID NO:38.
 94. A polynucleotide of claim 12, comprising the polynucleotide sequence of SEQ ID NO:39.
 95. A polynucleotide of claim 12, comprising the polynucleotide sequence of SEQ ID NO:40.
 96. A polynucleotide of claim 12, comprising the polynucleotide sentence of SEQ m NO:41.
 97. A polynucleotide of claim 12, comprising the polynucleotide sequence of SEQ ID NO:42. 